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Sample records for morphometry reveals reduced

  1. Source-based morphometry reveals distinct patterns of aberrant brain volume in delusional infestation.

    PubMed

    Wolf, Robert Ch; Huber, Markus; Lepping, Peter; Sambataro, Fabio; Depping, Malte S; Karner, Martin; Freudenmann, Roland W

    2014-01-03

    Little is known about the neural correlates of delusional infestation (DI), the delusional belief to be infested with pathogens. So far, evidence comes mainly from case reports and case series. We investigated brain morphology in 16 DI patients and 16 healthy controls using structural magnetic resonance imaging and a multivariate data analysis technique, i.e. source-based morphometry (SBM). In addition, we explored differences in brain structure in patient subgroups based on disease aetiology. SBM revealed two patterns exhibiting significantly (p<0.05, Bonferroni-corrected) lower grey and higher white matter volume in DI patients compared to controls. Lower grey matter volume was found in medial prefrontal cortex, anterior cingulate cortex, medial temporal lobe structures (parahippocampus and hippocampus), sensorimotor cortices, bilateral insula and thalamus and inferior parietal regions. Higher white matter volume was found in medial and middle frontal and temporal cortices, left insula and lentiform nucleus. Grey matter volume was abnormal in both "psychiatric" (primary DI and DI associated with an affective disorder) and "organic" DI (DI due to a medical condition). In contrast, aberrant white matter volume was only confirmed for the "organic" DI patient subgroup. These results suggest prefrontal, temporal, parietal, insular, thalamic and striatal dysfunction underlying DI. Moreover, the data suggest that aetiologically distinct presentations of DI share similar patterns of abnormal grey matter volume, whereas aberrant white matter volume appears to be restricted to organic cases. © 2013.

  2. Tensor-Based Morphometry Reveals Volumetric Deficits in Moderate=Severe Pediatric Traumatic Brain Injury

    PubMed Central

    Hua, Xue; Villalon-Reina, Julio; Moran, Lisa M.; Kernan, Claudia; Babikian, Talin; Mink, Richard; Babbitt, Christopher; Johnson, Jeffrey; Giza, Christopher C.; Thompson, Paul M.; Asarnow, Robert F.

    2016-01-01

    Abstract Traumatic brain injury (TBI) can cause widespread and prolonged brain degeneration. TBI can affect cognitive function and brain integrity for many years after injury, often with lasting effects in children, whose brains are still immature. Although TBI varies in how it affects different individuals, image analysis methods such as tensor-based morphometry (TBM) can reveal common areas of brain atrophy on magnetic resonance imaging (MRI), secondary effects of the initial injury, which will differ between subjects. Here we studied 36 pediatric moderate to severe TBI (msTBI) participants in the post-acute phase (1–6 months post-injury) and 18 msTBI participants who returned for their chronic assessment, along with well-matched controls at both time-points. Participants completed a battery of cognitive tests that we used to create a global cognitive performance score. Using TBM, we created three-dimensional (3D) maps of individual and group differences in regional brain volumes. At both the post-acute and chronic time-points, the greatest group differences were expansion of the lateral ventricles and reduction of the lingual gyrus in the TBI group. We found a number of smaller clusters of volume reduction in the cingulate gyrus, thalamus, and fusiform gyrus, and throughout the frontal, temporal, and parietal cortices. Additionally, we found extensive associations between our cognitive performance measure and regional brain volume. Our results indicate a pattern of atrophy still detectable 1-year post-injury, which may partially underlie the cognitive deficits frequently found in TBI. PMID:26393494

  3. [Grey matter concentration revealed by voxel-based morphometry in individuals with cognitive vulnerability to depression].

    PubMed

    Yuan, Shuwen; Lei, Hui; Yao, Shuqiao; Zhang, Xiaocui

    2017-06-28

    To explore the grey matter concentration in individuals with cognitive vulnerability to depression.
 Methods: Thirty individuals with cognitive vulnerability to depression and thirty age- and gender-matched healthy controls were enrolled in this study, and they were subjected to magnetic resonance imaging (MRI) examination. The grey matter concentration differences were compared between the two groups by using voxel-based morphometry (VBM) following MRI.
 Results: Individuals with cognitive vulnerability to depression showed significantly lower grey matter density in bilateral insular, left cerebellum, right supplementary motor area, and left precentral gyrus than those in the healthy controls, while the healthy controls showed significantly lower grey density in the right inferior frontal gyrus, right middle frontal gyrus, and left cuneus than those in the individuals with cognitive vulnerability to depression.
 Conclusion: Structural brain abnormalities in individuals with cognitive vulnerability to depression might be the neural basis for cognitive vulnerability to depression.

  4. Surface-based morphometry reveals the neuroanatomical basis of the five-factor model of personality.

    PubMed

    Riccelli, Roberta; Toschi, Nicola; Nigro, Salvatore; Terracciano, Antonio; Passamonti, Luca

    2017-01-24

    The five-factor model (FFM) is a widely used taxonomy of human personality; yet its neuro anatomical basis remains unclear. This is partly because past associations between gray-matter volume and FFM were driven by different surface-based morphometry (SBM) indices (i.e. cortical thickness, surface area, cortical folding or any combination of them). To overcome this limitation, we used Free-Surfer to study how variability in SBM measures was related to the FFM in n = 507 participants from the Human Connectome Project.Neuroticism was associated with thicker cortex and smaller area and folding in prefrontal-temporal regions. Extraversion was linked to thicker pre-cuneus and smaller superior temporal cortex area. Openness was linked to thinner cortex and greater area and folding in prefrontal-parietal regions. Agreeableness was correlated to thinner prefrontal cortex and smaller fusiform gyrus area. Conscientiousness was associated with thicker cortex and smaller area and folding in prefrontal regions. These findings demonstrate that anatomical variability in prefrontal cortices is linked to individual differences in the socio-cognitive dispositions described by the FFM. Cortical thickness and surface area/folding were inversely related each others as a function of different FFM traits (neuroticism, extraversion and consciousness vs openness), which may reflect brain maturational effects that predispose or protect against psychiatric disorders.

  5. Voxel-based morphometry reveals increased gray matter density in Broca's area in male symphony orchestra musicians.

    PubMed

    Sluming, Vanessa; Barrick, Thomas; Howard, Matthew; Cezayirli, Enis; Mayes, Andrew; Roberts, Neil

    2002-11-01

    Broca's area is a major neuroanatomical substrate for spoken language and various musically relevant abilities, including visuospatial and audiospatial localization. Sight reading is a musician-specific visuospatial analysis task, and spatial ability is known to be amenable to training effects. Musicians have been reported to perform significantly better than nonmusicians on spatial ability tests, which is supported by our findings with the Benton judgement of line orientation (JOL) test (P < 0.001). We hypothesised that use-dependent adaptation would lead to increased gray matter density in Broca's area in musicians. Voxel-based morphometry (VBM) and stereological analyses were applied to high-resolution 3D MR images in male orchestral musicians (n = 26) and sex, handedness, and IQ-matched nonmusicians (n = 26). The wide age range (26 to 66 years) of volunteers permitted a secondary analysis of age-related effects. VBM with small volume correction (SVC) revealed a significant (P = 0.002) region of increased gray matter in Broca's area in the left inferior frontal gyrus in musicians. We observed significant age-related volume reductions in cerebral hemispheres, dorsolateral prefrontal cortex subfields bilaterally and gray matter density in the left inferior frontal gyrus in controls but not musicians; a positive correlation between JOL test score and age in musicians but not controls; a positive correlation between years of playing and the volume of gray matter in a significant region identified by VBM in under-50-year-old musicians. We suggest that orchestral musical performance promotes use-dependent retention, and possibly expansion, of gray matter involving Broca's area and that this provides further support for shared neural substrates underpinning expressive output in music and language.

  6. Sexual dimorphism of sulcal morphology of the ferret cerebrum revealed by MRI-based sulcal surface morphometry

    PubMed Central

    Sawada, Kazuhiko; Horiuchi-Hirose, Miwa; Saito, Shigeyoshi; Aoki, Ichio

    2015-01-01

    The present study quantitatively assessed sexual dimorphism of cortical convolution and sulcal morphology in young adult ferrets by MRI-based sulcal surface morphometry. Ex vivo T1-weighted (short TR/TE) MRI of the ferret cerebrum was acquired with high spatial resolution at 7-tesla. The degree of cortical convolution, evaluated quantitatively based on 3D MRI data by sulcation index (SI), was significantly greater in males (0.553 ± 0.036) than in females (0.502 ± 0.043) (p < 0.001). The rostrocaudal distribution of the cortical convolution revealed a greater convolution in the frontal region of the cortex in males than in females and by a posterior extension of the convolution in the temporo-parieto-occipital region of males. Although the cerebral width in the frontal region was not different between sexes, the rhinal fissure and rostral region of splenial sulcus were more infolded in males than in females. On the contrary, the cerebral width was greater in males in the temporo-parieto-occipital region, and male-prominent posterior extension of infolding was noted in the lateral sulcus, caudal suprasylvian sulcus, pesudosylvian sulcus, hippocampal sulcus, and the caudal region of splenial sulcus. Notably, the caudal descending region of lateral sulcus was clearly infolded in males, but obscured in females. The present results suggest a region-related sexual dimorphism of the sulcal infolding, which is reflected by local cortical expansion in the ferret cerebrum. In particular, male-favored sulcal infolding with expansion of the temporo-parieto-occipital neocortex may be relevant to the human cerebral cortex regarding visuo-spatial and emotion processing, which are known to differ between sexes. The present results will provide fundamental information assessing sex-related changes in the regional sulcal infolding, when ferrets with experimentally-induced gyrification abnormality will be used as models for male-prevalent or male-earlier-onset neurodevelopmental

  7. Prospective motion correction with volumetric navigators (vNavs) reduces the bias and variance in brain morphometry induced by subject motion.

    PubMed

    Tisdall, M Dylan; Reuter, Martin; Qureshi, Abid; Buckner, Randy L; Fischl, Bruce; van der Kouwe, André J W

    2016-02-15

    Recent work has demonstrated that subject motion produces systematic biases in the metrics computed by widely used morphometry software packages, even when the motion is too small to produce noticeable image artifacts. In the common situation where the control population exhibits different behaviors in the scanner when compared to the experimental population, these systematic measurement biases may produce significant confounds for between-group analyses, leading to erroneous conclusions about group differences. While previous work has shown that prospective motion correction can improve perceived image quality, here we demonstrate that, in healthy subjects performing a variety of directed motions, the use of the volumetric navigator (vNav) prospective motion correction system significantly reduces the motion-induced bias and variance in morphometry. Copyright © 2015 Elsevier Inc. All rights reserved.

  8. Prospective motion correction with volumetric navigators (vNavs) reduces the bias and variance in brain morphometry induced by subject motion

    PubMed Central

    Tisdall, M. Dylan; Reuter, Martin; Qureshi, Abid; Buckner, Randy L.; Fischl, Bruce; van der Kouwe, André J. W.

    2015-01-01

    Recent work has demonstrated that subject motion produces systematic biases in the metrics computed by widely used morphometry software packages, even when the motion is too small to produce noticeable image artefacts. In the common situation where the control population exhibits different behaviours in the scanner when compared to the experimental population, these systematic measurement biases may produce significant confounds for between-group analyses, leading to erroneous conclusions about group differences. While previous work has shown that prospective motion correction can improve perceived image quality, here we demonstrate that, in healthy subjects performing a variety of directed motions, the use of the volumetric navigator (vNav) prospective motion correction system significantly reduces the motion-induced bias and variance in morphometry. PMID:26654788

  9. In vivo magnetic resonance images reveal neuroanatomical sex differences through the application of voxel-based morphometry in C57BL/6 mice.

    PubMed

    Meyer, Cassandra E; Kurth, Florian; Lepore, Stefano; Gao, Josephine L; Johnsonbaugh, Hadley; Oberoi, Mandavi R; Sawiak, Stephen J; MacKenzie-Graham, Allan

    2017-09-15

    Behaviorally relevant sex differences are often associated with structural differences in the brain and many diseases are sexually dimorphic in prevalence and progression. Characterizing sex differences is imperative to gaining a complete understanding of behavior and disease which will, in turn, allow for a balanced approach to scientific research and the development of therapies. In this study, we generated novel tissue probability maps (TPMs) based on 30 male and 30 female in vivo C57BL/6 mouse brain magnetic resonance images and used voxel-based morphometry (VBM) to analyze sex differences. Females displayed larger anterior hippocampus, basolateral amygdala, and lateral cerebellar cortex volumes, while males exhibited larger cerebral cortex, medial amygdala, and medial cerebellar cortex volumes. Atlas-based morphometry (ABM) revealed a statistically significant sex difference in cortical volume and no difference in whole cerebellar volume. This validated our VBM findings that showed a larger cerebral cortex in male mice and a pattern of dimorphism in the cerebellum where the lateral portion was larger in females and the medial portion was larger in males. These results are consonant with previous ex vivo studies examining sex differences, but also suggest further regions of interest. Copyright © 2017. Published by Elsevier Inc.

  10. Isotropic 3D Nuclear Morphometry of Normal, Fibrocystic and Malignant Breast Epithelial Cells Reveals New Structural Alterations

    PubMed Central

    Nandakumar, Vivek; Kelbauskas, Laimonas; Hernandez, Kathryn F.; Lintecum, Kelly M.; Senechal, Patti; Bussey, Kimberly J.; Davies, Paul C. W.; Johnson, Roger H.; Meldrum, Deirdre R.

    2012-01-01

    Background Grading schemes for breast cancer diagnosis are predominantly based on pathologists' qualitative assessment of altered nuclear structure from 2D brightfield microscopy images. However, cells are three-dimensional (3D) objects with features that are inherently 3D and thus poorly characterized in 2D. Our goal is to quantitatively characterize nuclear structure in 3D, assess its variation with malignancy, and investigate whether such variation correlates with standard nuclear grading criteria. Methodology We applied micro-optical computed tomographic imaging and automated 3D nuclear morphometry to quantify and compare morphological variations between human cell lines derived from normal, benign fibrocystic or malignant breast epithelium. To reproduce the appearance and contrast in clinical cytopathology images, we stained cells with hematoxylin and eosin and obtained 3D images of 150 individual stained cells of each cell type at sub-micron, isotropic resolution. Applying volumetric image analyses, we computed 42 3D morphological and textural descriptors of cellular and nuclear structure. Principal Findings We observed four distinct nuclear shape categories, the predominant being a mushroom cap shape. Cell and nuclear volumes increased from normal to fibrocystic to metastatic type, but there was little difference in the volume ratio of nucleus to cytoplasm (N/C ratio) between the lines. Abnormal cell nuclei had more nucleoli, markedly higher density and clumpier chromatin organization compared to normal. Nuclei of non-tumorigenic, fibrocystic cells exhibited larger textural variations than metastatic cell nuclei. At p<0.0025 by ANOVA and Kruskal-Wallis tests, 90% of our computed descriptors statistically differentiated control from abnormal cell populations, but only 69% of these features statistically differentiated the fibrocystic from the metastatic cell populations. Conclusions Our results provide a new perspective on nuclear structure variations

  11. Neuroanatomical differences in brain areas implicated in perceptual and other core features of autism revealed by cortical thickness analysis and voxel-based morphometry.

    PubMed

    Hyde, Krista L; Samson, Fabienne; Evans, Alan C; Mottron, Laurent

    2010-04-01

    Autism spectrum disorder is a complex neurodevelopmental variant thought to affect 1 in 166 [Fombonne (2003): J Autism Dev Disord 33:365-382]. Individuals with autism demonstrate atypical social interaction, communication, and repetitive behaviors, but can also present enhanced abilities, particularly in auditory and visual perception and nonverbal reasoning. Structural brain differences have been reported in autism, in terms of increased total brain volume (particularly in young children with autism), and regional gray/white matter differences in both adults and children with autism, but the reports are inconsistent [Amaral et al. (2008): Trends Neurosci 31:137-145]. These inconsistencies may be due to differences in diagnostic/inclusion criteria, and age and Intelligence Quotient of participants. Here, for the first time, we used two complementary magnetic resonance imaging techniques, cortical thickness analyses, and voxel-based morphometry (VBM), to investigate the neuroanatomical differences between a homogenous group of young adults with autism of average intelligence but delayed or atypical language development (often referred to as "high-functioning autism"), relative to a closely matched group of typically developing controls. The cortical thickness and VBM techniques both revealed regional structural brain differences (mostly in terms of gray matter increases) in brain areas implicated in social cognition, communication, and repetitive behaviors, and thus in each of the core atypical features of autism. Gray matter increases were also found in auditory and visual primary and associative perceptual areas. We interpret these results as the first structural brain correlates of atypical auditory and visual perception in autism, in support of the enhanced perceptual functioning model [Mottron et al. (2006): J Autism Dev Disord 36:27-43].

  12. Quantitative morphometry of electrophysiologically identified CA3b interneurons reveals robust local geometry and distinct cell classes.

    PubMed

    Ascoli, Giorgio A; Brown, Kerry M; Calixto, Eduardo; Card, J Patrick; Galván, E J; Perez-Rosello, T; Barrionuevo, Germán

    2009-08-20

    The morphological and electrophysiological diversity of inhibitory cells in hippocampal area CA3 may underlie specific computational roles and is not yet fully elucidated. In particular, interneurons with somata in strata radiatum (R) and lacunosum-moleculare (L-M) receive converging stimulation from the dentate gyrus and entorhinal cortex as well as within CA3. Although these cells express different forms of synaptic plasticity, their axonal trees and connectivity are still largely unknown. We investigated the branching and spatial patterns, plus the membrane and synaptic properties, of rat CA3b R and L-M interneurons digitally reconstructed after intracellular labeling. We found considerable variability within but no difference between the two layers, and no correlation between morphological and biophysical properties. Nevertheless, two cell types were identified based on the number of dendritic bifurcations, with significantly different anatomical and electrophysiological features. Axons generally branched an order of magnitude more than dendrites. However, interneurons on both sides of the R/L-M boundary revealed surprisingly modular axodendritic arborizations with consistently uniform local branch geometry. Both axons and dendrites followed a lamellar organization, and axons displayed a spatial preference toward the fissure. Moreover, only a small fraction of the axonal arbor extended to the outer portion of the invaded volume, and tended to return toward the proximal region. In contrast, dendritic trees demonstrated more limited but isotropic volume occupancy. These results suggest a role of predominantly local feedforward and lateral inhibitory control for both R and L-M interneurons. Such a role may be essential to balance the extensive recurrent excitation of area CA3 underlying hippocampal autoassociative memory function.

  13. Patterns of Quaternary uplift of the Corinth rift southern border (N Peloponnese, Greece) revealed by fluvial landscape morphometry

    NASA Astrophysics Data System (ADS)

    Demoulin, A.; Beckers, A.; Hubert-Ferrari, A.

    2015-10-01

    The Rift of Corinth is a world-class example of young active rifting and, as such, is an ideal natural laboratory of continental extension. However, though much investigated for two decades, several aspects of the mechanisms at work are still poorly understood. The aim of this paper is a detailed morphometric study of the fluvial landscape response to the tectonic uplift of the rift southern shoulder in order to reconstruct the rift's Quaternary evolution, with special attention to timing, location, and intensity of uplift episodes. Based on the use of a large set of catchment and long profile metrics complemented by the new R/SR integrative approach of the regional drainage network, we identified three distinct episodes of uplift of the northern Peloponnese coastal tract, of which the intermediate one, dated around 0.35-0.4 Ma, is only recorded in the topography of the central part of the rift shoulder, and the youngest one appears to have propagated from east to west over the last 10-20 ka. While net uplift remained minimum in the eastern part of the study area during the whole Quaternary, it shows a clear maximum in the central part of the rift shoulder since 0.4 Ma and an eastward shift of this maximum in recent times. Maximum uplift rates calculated from the morphometric data are of > 1.05 and 2-5 mm year- 1 for, the mid-Middle Pleistocene and Holocene uplift episodes, respectively. The morphometric evidence reveals an onshore uplift history remarkably consistent with the rift evolution reconstructed from other data sets. In the long term, it shows a stable pattern of maximum activity in the central part of the rift, confirming previous conclusions about the absence of rift propagation. In the short term, it sheds light on a possible E-W migration of the zone of recent uplift, suggesting that in the near future fault activity and seismic hazard might concentrate in the Heliki-Aegion area, at the western tip of this uplift wave.

  14. Dissociations in Cortical Morphometry in Youth with Down Syndrome: Evidence for Reduced Surface Area but Increased Thickness.

    PubMed

    Lee, Nancy Raitano; Adeyemi, Elizabeth I; Lin, Amy; Clasen, Liv S; Lalonde, François M; Condon, Ellen; Driver, David I; Shaw, Philip; Gogtay, Nitin; Raznahan, Armin; Giedd, Jay N

    2016-07-01

    Detailed descriptions of cortical anatomy in youth with Down syndrome (DS), the most common genetic cause of intellectual disability (ID), are scant. Thus, the current study examined deviations in cortical thickness (CT) and surface area (SA), at high spatial resolution, in youth with DS, to identify focal differences relative to typically developing (TD) youth. Participants included 31 youth with DS and 45 age- and sex-matched TD controls (mean age ∼16 years; range = 5-24 years). All participants completed T1-weighted ASSET-calibrated magnetization prepared rapid gradient echo scans on a 3-T magnetic resonance imaging scanner. Replicating prior investigations, cortical volume was reduced in DS compared with controls. However, a novel dissociation for SA and CT was found-namely, SA was reduced (predominantly in frontal and temporal regions) while CT was increased (notably in several regions thought to belong to the default mode network; DMN). These findings suggest that reductions in SA rather than CT are driving the cortical volume reductions reported in prior investigations of DS. Moreover, given the link between DMN functionality and Alzheimer's symptomatology in chromosomally typical populations, future DS studies may benefit from focusing on the cortex in DMN regions, as such investigations may provide clues to the precocious onset of Alzheimer's disease in this at-risk group.

  15. Mammalian sperm morphometry.

    PubMed Central

    Gage, M J

    1998-01-01

    Understanding the adaptive significance of sperm form and function has been a challenge to biologists because sperm are highly specialized cells operating at a microscopic level in a complex environment. A fruitful course of investigation has been to use the comparative approach. This comparative study attempts to address some fundamental questions of the evolution of mammalian sperm morphometry. Data on sperm morphometry for 445 mammalian species were collated from published sources. I use contemporary phylogenetic analysis to control for the inherent non-independence of species and explore relationships between the morphometric dimensions of the three essential spermatozoal components: head, mid-piece and flagellum. Energy for flagellar action is metabolized by the mitochondrial-dense mid-piece and these combine to propel the sperm head, carrying the male haplotype, to the ovum. I therefore search for evolutionary associations between sperm morphometry and body mass, karyotype and the duration of oestrus. In contrast to previous findings, there is no inverse correlation between body weight and sperm length. Sperm mid-piece and flagellum lengths are positively associated with both head length and area, and the slopes of these relationships are discussed. Flagellum length is positively associated with mid-piece length but, in contrast to previous research and after phylogenetic control, I find no relationship between flagellum length and the volume of the mitochondrial sheath. Sperm head dimensions are not related to either genome mass or chromosome number, and there are no relationships between sperm morphometry and the duration of oestrus. PMID:9474794

  16. Brain morphometry of Dravet syndrome.

    PubMed

    Pérez, Alejandro; García-Pentón, Lorna; Canales-Rodríguez, Erick J; Lerma-Usabiaga, Garikoitz; Iturria-Medina, Yasser; Román, Francisco J; Davidson, Doug; Alemán-Gómez, Yasser; Acha, Joana; Carreiras, Manuel

    2014-10-01

    The aim of this study was to identify differential global and local brain structural patterns in Dravet Syndrome (DS) patients as compared with a control subject group, using brain morphometry techniques which provide a quantitative whole-brain structural analysis that allows for specific patterns to be generalized across series of individuals. Nine patients with the diagnosis of DS that tested positive for mutation in the SCN1A gene and nine well-matched healthy controls were investigated using voxel brain morphometry (VBM), cortical thickness and cortical gyrification measurements. Global volume reductions of gray matter (GM) and white matter (WM) were related to DS. Local volume reductions corresponding to several white matter regions in brainstem, cerebellum, corpus callosum, corticospinal tracts and association fibers (left inferior fronto-occipital fasciculus and left uncinate fasciculus) were also found. Furthermore, DS showed a reduced cortical folding in the right precentral gyrus. The present findings describe DS-related brain structure abnormalities probably linked to the expression of the SCN1A mutation. Copyright © 2014 Elsevier B.V. All rights reserved.

  17. Atlas warping for brain morphometry

    NASA Astrophysics Data System (ADS)

    Machado, Alexei M. C.; Gee, James C.

    1998-06-01

    In this work, we describe an automated approach to morphometry based on spatial normalizations of the data, and demonstrate its application to the analysis of gender differences in the human corpus callosum. The purpose is to describe a population by a reduced and representative set of variables, from which a prior model can be constructed. Our approach is rooted in the assumption that individual anatomies can be considered as quantitative variations on a common underlying qualitative plane. We can therefore imagine that a given individual's anatomy is a warped version of some referential anatomy, also known as an atlas. The spatial warps which transform a labeled atlas into anatomic alignment with a population yield immediate knowledge about organ size and shape in the group. Furthermore, variation within the set of spatial warps is directly related to the anatomic variation among the subjects. Specifically, the shape statistics--mean and variance of the mappings--for the population can be calculated in a special basis, and an eigendecomposition of the variance performed to identify the most significant modes of shape variation. The results obtained with the corpus callosum study confirm the existence of substantial anatomical differences between males and females, as reported in previous experimental work.

  18. Revealing and reducing uncertainties in climate impact assessments

    NASA Astrophysics Data System (ADS)

    Clark, M. P.

    2015-12-01

    Water resources planning and management involves understanding the vulnerability of water resource systems to a wide range of different stresses. A key responsibility is to identify defensible options for the design and management of systems under an uncertain and changing climate. In the water resources sector this requires defining a range of different climate change narratives in order to evaluate the vulnerability of infrastructure and the effectiveness of different management strategies to climate-related stresses. Recent research is just now beginning to reveal how different methodological choices can impact portrayals of climate risk. We present research showing that the common approaches to climate change assessments in the water sector are affected by substantial uncertainties in methods used for climate downscaling and hydrologic modeling, and suggest that many of these uncertainties are reducible. For example, improving continental scale hydrologic model parameters can reduce one source of uncertainty. We also present research to improve characterization of uncertainty, in order to reduce the extent to which the portrayal of climate change impacts depends on ad hoc methodological choices and provide a holistic estimate of the degree to which the climate change signal emerges from the envelope of uncertainty. We hope that this presentation stimulates discussion on the best practices for climate impact assessments, and ways to improve the robustness of water resources planning under a changing climate.

  19. Voxel-based morphometry and arterial spin labeling fMRI reveal neuropathic and neuroplastic features of brain processing of itch in end-stage renal disease.

    PubMed

    Papoiu, Alexandru D P; Emerson, Nichole M; Patel, Tejesh S; Kraft, Robert A; Valdes-Rodriguez, Rodrigo; Nattkemper, Leigh A; Coghill, Robert C; Yosipovitch, Gil

    2014-10-01

    Pruritus of end-stage renal disease (ESRD) is a multifactorial symptom of complex etiology not yet fully understood. In this study we have investigated the cerebral perfusion patterns at rest in ESRD patients on hemodialysis, compared with those in healthy volunteers. We have also studied the brain responses evoked by experimental itch induction in ESRD, after stimulating the two distinct histamine and cowhage itch pathways, and compared them with the responses evoked in healthy volunteers. To identify potential structural alterations in ESRD patients compared with a group of age-matched healthy volunteers, we calculated the density of gray matter for the entire brain using a voxel-based morphometric analysis. Our results indicated that gray matter density was significantly reduced in ESRD patients in the frontal, parietal, temporal, and occipital cortices, as well as in the S1, precuneus, and insula, whereas the brain stem, hippocampus, amygdala, midcingulate cortex, and nucleus accumbens displayed an increased gray matter density. Functionally, we found a significantly higher brain perfusion at baseline associated with ESRD pruritus in the anterior cingulate, insula, claustrum, hippocampus, and nucleus accumbens. The brain responses evoked by cowhage itch, which are mediated by protease-activated receptors (PAR2), displayed significant differences compared with responses in healthy individuals and were correlated with perceived itch intensity in a dual, complex manner. The inverse correlations in particular suggested that a negative feedback mechanism modulated itch intensity, when elicited in a preexistent chronic itch background.

  20. Mindboggling morphometry of human brains

    PubMed Central

    Bao, Forrest S.; Giard, Joachim; Stavsky, Eliezer; Lee, Noah; Rossa, Brian; Reuter, Martin; Chaibub Neto, Elias

    2017-01-01

    Mindboggle (http://mindboggle.info) is an open source brain morphometry platform that takes in preprocessed T1-weighted MRI data and outputs volume, surface, and tabular data containing label, feature, and shape information for further analysis. In this article, we document the software and demonstrate its use in studies of shape variation in healthy and diseased humans. The number of different shape measures and the size of the populations make this the largest and most detailed shape analysis of human brains ever conducted. Brain image morphometry shows great potential for providing much-needed biological markers for diagnosing, tracking, and predicting progression of mental health disorders. Very few software algorithms provide more than measures of volume and cortical thickness, while more subtle shape measures may provide more sensitive and specific biomarkers. Mindboggle computes a variety of (primarily surface-based) shapes: area, volume, thickness, curvature, depth, Laplace-Beltrami spectra, Zernike moments, etc. We evaluate Mindboggle’s algorithms using the largest set of manually labeled, publicly available brain images in the world and compare them against state-of-the-art algorithms where they exist. All data, code, and results of these evaluations are publicly available. PMID:28231282

  1. Cortical morphometry in frontoparietal and default mode networks in math-gifted adolescents.

    PubMed

    Navas-Sánchez, Francisco J; Carmona, Susana; Alemán-Gómez, Yasser; Sánchez-González, Javier; Guzmán-de-Villoria, Juan; Franco, Carolina; Robles, Olalla; Arango, Celso; Desco, Manuel

    2016-05-01

    Math-gifted subjects are characterized by above-age performance in intelligence tests, exceptional creativity, and high task commitment. Neuroimaging studies reveal enhanced functional brain organization and white matter microstructure in the frontoparietal executive network of math-gifted individuals. However, the cortical morphometry of these subjects remains largely unknown. The main goal of this study was to compare the cortical morphometry of math-gifted adolescents with that of an age- and IQ-matched control group. We used surface-based methods to perform a vertex-wise analysis of cortical thickness and surface area. Our results show that math-gifted adolescents present a thinner cortex and a larger surface area in key regions of the frontoparietal and default mode networks, which are involved in executive processing and creative thinking, respectively. The combination of reduced cortical thickness and larger surface area suggests above-age neural maturation of these networks in math-gifted individuals. Hum Brain Mapp 37:1893-1902, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  2. Voxel-based morphometry in patients with cryptogenic occipital epilepsies. Preliminary data.

    PubMed

    Bilo, L; De Leva, M F; Meo, R; Tortora, F; Esposito, F; Aragri, A; Elefante, A

    2010-03-01

    We evaluated the differences in grey matter concentration (GMC) by voxel-based morphometry (VBM) in patients with cryptogenic occipital epilepsies. VBM analysis was performed in 11 patients with cryptogenic occipital epilepsies compared to 11 healthy controls. VBM analysis in patients revealed focal areas of reduced GMC in the occipital cortex and, more interestingly, increased GMC in the midbrain tegmentum and basal ganglia (globus pallidus and thalamus). VBM may disclose slight structural abnormalities in the brain of cryptogenic epilepsy patients, not evident with standard MRI. To the best of our knowledge, this is the first literature report describing areas of altered GMC in patients with occipital epilepsy. We hypothesize that these findings might be related to epileptic discharges and/or their diffusion and suggest that midbrain, globus pallidus and thalamus may be part of a functional network originating from the occipital areas.

  3. Facial three-dimensional morphometry.

    PubMed

    Ferrario, V F; Sforza, C; Poggio, C E; Serrao, G

    1996-01-01

    Three-dimensional facial morphometry was investigated in a sample of 40 men and 40 women, with a new noninvasive computerized method. Subjects ranged in age between 19 and 32 years, had sound dentitions, and no craniocervical disorders. For each subject, 16 cutaneous facial landmarks were automatically collected by a system consisting of two infrared camera coupled device (CCD) cameras, real time hardware for the recognition of markers, and software for the three-dimensional reconstruction of landmarks' x, y, z coordinates. From these landmarks, 15 linear and 10 angular measurements, and four linear distance ratios were computed and averaged for sex. For all angular values, both samples showed a narrow variability and no significant gender differences were demonstrated. Conversely, all the linear measurements were significantly higher in men than in women. The highest intersample variability was observed for the measurements of facial height (prevalent vertical dimension), and the lowest for the measurements of facial depth (prevalent horizontal dimension). The proportions of upper and lower face height relative to the anterior face height showed a significant sex difference. Mean values were in good agreement with literature data collected with traditional methods. The described method allowed the direct and noninvasive calculation of three-dimensional linear and angular measurements that would be usefully applied in clinics as a supplement to the classic x-ray cephalometric analyses.

  4. Comparative Minicolumnar Morphometry of Three Distinguished Scientists

    ERIC Educational Resources Information Center

    Casanova, Manuel F.; Switala, Andrew E.; Trippe, Juan; Fitzgerald, Michael

    2007-01-01

    It has been suggested that the cell minicolumn is the smallest module capable of information processing within the brain. In this case series, photomicrographs of six regions of interests (Brodmann areas 4, 9, 17, 21, 22, and 40) were analyzed by computerized image analysis for minicolumnar morphometry in the brains of three distinguished…

  5. Comparative Minicolumnar Morphometry of Three Distinguished Scientists

    ERIC Educational Resources Information Center

    Casanova, Manuel F.; Switala, Andrew E.; Trippe, Juan; Fitzgerald, Michael

    2007-01-01

    It has been suggested that the cell minicolumn is the smallest module capable of information processing within the brain. In this case series, photomicrographs of six regions of interests (Brodmann areas 4, 9, 17, 21, 22, and 40) were analyzed by computerized image analysis for minicolumnar morphometry in the brains of three distinguished…

  6. The effect of selected staining techniques on bull sperm morphometry.

    PubMed

    Banaszewska, Dorota; Andraszek, Katarzyna; Czubaszek, Magdalena; Biesiada-Drzazga, Barbara

    2015-08-01

    Sperm morphometry has some value as an indicator of reproductive capacity in males. In laboratory practice a variety of slide-staining methods are used during morphological evaluation of semen to predict male fertility. The aim of this study was to determine the effect of staining of semen using four different techniques on the morphometry of the bull sperm cell. The material for the study consisted of semen collected from test bulls of the Black-and-White variety of Holstein-Friesians. The results obtained in the study indicate differences in the dimensions of bull sperm heads when different slide staining techniques were used. The most similar results for sperm head dimensions were obtained in the case of SpermBlue(®) and eosin+gentian violet complex, although statistically significant differences were found between all the staining techniques. Extreme values were noted for the other staining techniques - lowest for the Papanicolaou and highest for silver nitrate, which may indicate more interference in the cell by the reagents used in the staining process. However, silver nitrate staining was best at identifying the structures of the sperm cell. Hence it is difficult to determine which of the staining methods most faithfully reveals the dimensions and shape of the bull sperm. Copyright © 2015 Elsevier B.V. All rights reserved.

  7. Mapping abnormal subcortical brain morphometry in an elderly HIV + cohort

    PubMed Central

    Wade, Benjamin S.C.; Valcour, Victor G.; Wendelken-Riegelhaupt, Lauren; Esmaeili-Firidouni, Pardis; Joshi, Shantanu H.; Gutman, Boris A.; Thompson, Paul M.

    2015-01-01

    Over 50% of HIV + individuals exhibit neurocognitive impairment and subcortical atrophy, but the profile of brain abnormalities associated with HIV is still poorly understood. Using surface-based shape analyses, we mapped the 3D profile of subcortical morphometry in 63 elderly HIV + participants and 31 uninfected controls. The thalamus, caudate, putamen, pallidum, hippocampus, amygdala, brainstem, accumbens, callosum and ventricles were segmented from high-resolution MRIs. To investigate shape-based morphometry, we analyzed the Jacobian determinant (JD) and radial distances (RD) defined on each region's surfaces. We also investigated effects of nadir CD4 + T-cell counts, viral load, time since diagnosis (TSD) and cognition on subcortical morphology. Lastly, we explored whether HIV + participants were distinguishable from unaffected controls in a machine learning context. All shape and volume features were included in a random forest (RF) model. The model was validated with 2-fold cross-validation. Volumes of HIV + participants' bilateral thalamus, left pallidum, left putamen and callosum were significantly reduced while ventricular spaces were enlarged. Significant shape variation was associated with HIV status, TSD and the Wechsler adult intelligence scale. HIV + people had diffuse atrophy, particularly in the caudate, putamen, hippocampus and thalamus. Unexpectedly, extended TSD was associated with increased thickness of the anterior right pallidum. In the classification of HIV + participants vs. controls, our RF model attained an area under the curve of 72%. PMID:26640768

  8. Evolutionary sperm morphology and morphometry in armadillos.

    PubMed

    Cetica, P D; Solari, A J; Merani, M S; De Rosas, J C; Burgos, M H

    1998-04-01

    Little is known about the evolution of vertebrate spermatozoa. In most eutherian taxa a high degree of uniformity in sperm shapes and dimensions among species was observed. The aim of this work is to trace a possible evolutionary change in sperm morphology and morphometry in dasypodids. The main difference between the spermatozoa of the studied armadillos is the shape of the sperm heads. We have classified the spermatozoa into 4 different groups according with their head shapes. Sperm from group 1 (Dasypus) are considered ancestral and are clearly separated from the others. The remaining sperm types are derivative ones; those from group 2 (Tolypeutes) are farther from those of groups 3 (Priodontes and Cabassous) and 4 (Chaetopractus, Zaedyus and Euphractus) which would have recently differentiated from each other. The sperm shape and size are not constant across taxa in armadillos; an important evolutive differentiation was established on the sperm morphology and morphometry between the different genera in Dasypodidae.

  9. The evolution of sperm morphometry in pheasants.

    PubMed

    Immler, S; Saint-Jalme, M; Lesobre, L; Sorci, G; Roman, Y; Birkhead, T R

    2007-05-01

    Post-copulatory sexual selection is thought to be a potent evolutionary force driving the diversification of sperm shape and function across species. In birds, insemination and fertilization are separated in time and sperm storage increases the duration of sperm-female interaction and hence the opportunity for sperm competition and cryptic female choice. We performed a comparative study of 24 pheasant species (Phasianidae, Galliformes) to establish the relative importance of sperm competition and the duration of sperm storage for the evolution of sperm morphometry (i.e. size of different sperm traits). We found that sperm size traits were negatively associated with the duration of sperm storage but were independent of the risk of sperm competition estimated from relative testis mass. Our study emphasizes the importance of female reproductive biology for the evolution of sperm morphometry particularly in sperm-storing taxa.

  10. Multitaxon activity profiling reveals differential microbial response to reduced seawater pH and oil pollution.

    PubMed

    Coelho, Francisco J R C; Cleary, Daniel F R; Costa, Rodrigo; Ferreira, Marina; Polónia, Ana R M; Silva, Artur M S; Simões, Mário M Q; Oliveira, Vanessa; Gomes, Newton C M

    2016-09-01

    There is growing concern that predicted changes to global ocean chemistry will interact with anthropogenic pollution to significantly alter marine microbial composition and function. However, knowledge of the compounding effects of climate change stressors and anthropogenic pollution is limited. Here, we used 16S and 18S rRNA (cDNA)-based activity profiling to investigate the differential responses of selected microbial taxa to ocean acidification and oil hydrocarbon contamination under controlled laboratory conditions. Our results revealed that a lower relative abundance of sulphate-reducing bacteria (Desulfosarcina/Desulfococcus clade) due to an adverse effect of seawater acidification and oil hydrocarbon contamination (reduced pH-oil treatment) may be coupled to changes in sediment archaeal communities. In particular, we observed a pronounced compositional shift and marked reduction in the prevalence of otherwise abundant operational taxonomic units (OTUs) belonging to the archaeal Marine Benthic Group B and Marine Hydrothermal Vent Group (MHVG) in the reduced pH-oil treatment. Conversely, the abundance of several putative hydrocarbonoclastic fungal OTUs was higher in the reduced pH-oil treatment. Sediment hydrocarbon profiling, furthermore, revealed higher concentrations of several alkanes in the reduced pH-oil treatment, corroborating the functional implications of the structural changes to microbial community composition. Collectively, our results advance the understanding of the response of a complex microbial community to the interaction between reduced pH and anthropogenic pollution. In future acidified marine environments, oil hydrocarbon contamination may alter the typical mixotrophic and k-/r-strategist composition of surface sediment microbiomes towards a more heterotrophic state with lower doubling rates, thereby impairing the ability of the ecosystem to recover from acute oil contamination events.

  11. Voxel-based morphometry evaluation of patients with photosensitive juvenile myoclonic epilepsy.

    PubMed

    Lin, Katia; Jackowski, Andrea Parolin; Carrete, Henrique; de Araújo Filho, Gerardo Maria; Silva, Henrique Hattori; Guaranha, Mirian Salvadori Bittar; Guilhoto, Laura Maria Figueiredo Ferreira; Bressan, Rodrigo Affonseca; Yacubian, Elza Márcia Targas

    2009-10-01

    We aim to investigate structural brain abnormalities in juvenile myoclonic epilepsy (JME) patients with photosensitivity (PS). Sixty JME patients, 19 (32%) of whom were photosensitive, were submitted to 1.5T magnetic resonance voxel-based morphometry (VBM). The control group (CTL) consisted of 30 sex-matched healthy volunteers. JME patients with (JME-PS) and without (JME-NPS) PS did not differ in their duration of disease, treatment or seizure control. VBM revealed significantly reduced bilateral gray matter volume (GMV) in thalami, insula cortices and cerebellar hemispheres; while significantly increased GMV was observed in the right superior frontal, orbitofrontal and medial frontal gyri of the JME group compared to CTL. JME-PS had reduced bilateral GMV of visual cortices when compared with CTL; while it was not seen among JME-NPS patients. Reduced left hippocampus and left inferior frontal gyrus volume was observed among JME-PS compared with JME-NPS. This study demonstrates structural abnormalities beyond the limits of the frontal lobes and provides evidence for the role of the occipital cortex in human PS, reinforcing the existence of functional-anatomic ictogenic networks in JME and the concept of 'system epilepsies'.

  12. REVEAL: An Extensible Reduced Order Model Builder for Simulation and Modeling

    SciTech Connect

    Agarwal, Khushbu; Sharma, Poorva; Ma, Jinliang; Lo, Chaomei; Gorton, Ian; Liu, Yan

    2013-04-30

    Many science domains need to build computationally efficient and accurate representations of high fidelity, computationally expensive simulations. These computationally efficient versions are known as reduced-order models. This paper presents the design and implementation of a novel reduced-order model (ROM) builder, the REVEAL toolset. This toolset generates ROMs based on science- and engineering-domain specific simulations executed on high performance computing (HPC) platforms. The toolset encompasses a range of sampling and regression methods that can be used to generate a ROM, automatically quantifies the ROM accuracy, and provides support for an iterative approach to improve ROM accuracy. REVEAL is designed to be extensible in order to utilize the core functionality with any simulator that has published input and output formats. It also defines programmatic interfaces to include new sampling and regression techniques so that users can ‘mix and match’ mathematical techniques to best suit the characteristics of their model. In this paper, we describe the architecture of REVEAL and demonstrate its usage with a computational fluid dynamics model used in carbon capture.

  13. STUDYING VENTRICULAR ABNORMALITIES IN MILD COGNITIVE IMPAIRMENT WITH HYPERBOLIC RICCI FLOW AND TENSOR-BASED MORPHOMETRY

    PubMed Central

    Shi, Jie; Stonnington, Cynthia M.; Thompson, Paul M.; Chen, Kewei; Gutman, Boris; Reschke, Cole; Baxter, Leslie C.; Reiman, Eric M.; Caselli, Richard J.; Wang, Yalin

    2014-01-01

    Mild Cognitive Impairment (MCI) is a transitional stage between normal aging and dementia and people with MCI are at high risk of progression to dementia. MCI is attracting increasing attention, as it offers an opportunity to target the disease process during an early symptomatic stage. Structural magnetic resonance imaging (MRI) measures have been the mainstay of Alzheimer’s disease (AD) imaging research, however, ventricular morphometry analysis remains challenging because of its complicated topological structure. Here we describe a novel ventricular morphometry system based on the hyperbolic Ricci flow method and tensor-based morphometry (TBM) statistics. Unlike prior ventricular surface parameterization methods, hyperbolic conformal parameterization is angle-preserving and does not have any singularities. Our system generates a one-to-one diffeomorphic mapping between ventricular surfaces with consistent boundary matching conditions. The TBM statistics encode a great deal of surface deformation information that could be inaccessible or overlooked by other methods. We applied our system to the baseline MRI scans of a set of MCI subjects from the Alzheimer’s Disease Neuroimaging Initiative (ADNI: 71 MCI converters vs. 62 MCI stable). Although the combined ventricular area and volume features did not differ between the two groups, our fine-grained surface analysis revealed significant differences in the ventricular regions close to the temporal lobe and posterior cingulate, structures that are affected early in AD. Significant correlations were also detected between ventricular morphometry, neuropsychological measures, and a previously described imaging index based on fluorodeoxyglucose positron emission tomography (FDG-PET) scans. This novel ventricular morphometry method may offer a new and more sensitive approach to study preclinical and early symptomatic stage AD. PMID:25285374

  14. Studying ventricular abnormalities in mild cognitive impairment with hyperbolic Ricci flow and tensor-based morphometry.

    PubMed

    Shi, Jie; Stonnington, Cynthia M; Thompson, Paul M; Chen, Kewei; Gutman, Boris; Reschke, Cole; Baxter, Leslie C; Reiman, Eric M; Caselli, Richard J; Wang, Yalin

    2015-01-01

    Mild Cognitive Impairment (MCI) is a transitional stage between normal aging and dementia and people with MCI are at high risk of progression to dementia. MCI is attracting increasing attention, as it offers an opportunity to target the disease process during an early symptomatic stage. Structural magnetic resonance imaging (MRI) measures have been the mainstay of Alzheimer's disease (AD) imaging research, however, ventricular morphometry analysis remains challenging because of its complicated topological structure. Here we describe a novel ventricular morphometry system based on the hyperbolic Ricci flow method and tensor-based morphometry (TBM) statistics. Unlike prior ventricular surface parameterization methods, hyperbolic conformal parameterization is angle-preserving and does not have any singularities. Our system generates a one-to-one diffeomorphic mapping between ventricular surfaces with consistent boundary matching conditions. The TBM statistics encode a great deal of surface deformation information that could be inaccessible or overlooked by other methods. We applied our system to the baseline MRI scans of a set of MCI subjects from the Alzheimer's Disease Neuroimaging Initiative (ADNI: 71 MCI converters vs. 62 MCI stable). Although the combined ventricular area and volume features did not differ between the two groups, our fine-grained surface analysis revealed significant differences in the ventricular regions close to the temporal lobe and posterior cingulate, structures that are affected early in AD. Significant correlations were also detected between ventricular morphometry, neuropsychological measures, and a previously described imaging index based on fluorodeoxyglucose positron emission tomography (FDG-PET) scans. This novel ventricular morphometry method may offer a new and more sensitive approach to study preclinical and early symptomatic stage AD.

  15. Fractal morphometry of cell complexity.

    PubMed

    Losa, Gabriele A

    2002-01-01

    Irregularity and self-similarity under scale changes are the main attributes of the morphological complexity of both normal and abnormal cells and tissues. In other words, the shape of a self-similar object does not change when the scale of measurement changes, because each part of it looks similar to the original object. However, the size and geometrical parameters of an irregular object do differ when it is examined at increasing resolution, which reveals more details. Significant progress has been made over the past three decades in understanding how irregular shapes and structures in the physical and biological sciences can be analysed. Dominant influences have been the discovery of a new practical geometry of Nature, now known as fractal geometry, and the continuous improvements in computation capabilities. Unlike conventional Euclidean geometry, which was developed to describe regular and ideal geometrical shapes which are practically unknown in nature, fractal geometry can be used to measure the fractal dimension, contour length, surface area and other dimension parameters of almost all irregular and complex biological tissues. We have used selected examples to illustrate the application of the fractal principle to measuring irregular and complex membrane ultrastructures of cells at specific functional and pathological stage.

  16. Brain Morphometry using MRI in Schizophrenia Patients

    NASA Astrophysics Data System (ADS)

    Abanshina, I.; Pirogov, Yu.; Kupriyanov, D.; Orlova, V.

    2010-01-01

    Schizophrenia has been the focus of intense neuroimaging research. Although its fundamental pathobiology remains elusive, neuroimaging studies provide evidence of abnormalities of cerebral structure and function in patients with schizophrenia. We used morphometry as a quantitative method for estimation of volume of brain structures. Seventy eight right-handed subjects aged 18-45 years were exposed to MRI-examination. Patients were divided into 3 groups: patients with schizophrenia, their relatives and healthy controls. The volumes of interested structures (caudate nucleus, putamen, ventricles, frontal and temporal lobe) were measured using T2-weighted MR-images. Correlations between structural differences and functional deficit were evaluated.

  17. Phylogeography of the intertidal copepod Tigriopus californicus reveals substantially reduced population differentiation at northern latitudes.

    PubMed

    Edmands, S

    2001-07-01

    Previous studies of the intertidal copepod Tigriopus californicus revealed one of the highest levels of mitochondrial DNA differentiation ever reported among conspecific populations. The present study extends the geographical sampling northward, adding populations from northern California to south-east Alaska. The mitochondrial phylogeny for the entire species range, based on cytochrome oxidase I sequences for a total of 49 individuals from 27 populations, again shows extreme differentiation among populations (up to 23%). However, populations from Oregon northwards appear to be derived and have interpopulation divergences five times lower than those between southern populations. Furthermore, although few individuals were sequenced from each locality, populations from Puget Sound northward had significantly reduced levels of within-population variation. These patterns are hypothesized to result from the contraction and expansion of populations driven by recent ice ages.

  18. Impact of udder and teat morphometry on udder health in Tharparkar cows under climatic condition of hot arid region of Thar Desert.

    PubMed

    Sharma, Amit; Sharma, Sanjita; Singh, Navav; Sharma, Vishnu; Pal, Rahul Singh

    2016-12-01

    Prevention of subclinical mastitis (SCM) is an important tool for sustainable dairying and implementing higher production level in animals. The present investigation involved a total of 397 quarters of milk examination of 105 indigenous Tharparkar cows at Livestock Research Centre, Chandan located in the Jaisalmer district of Rajasthan in Thar Desert to study the impact of udder and teat morphometry on udder health. Udder health was examined by somatic cell count to check the status of subclinical mastitis while udder and teat morphometry of 90 udder and 386 quarters, i.e., udder shape and depth, teat end shape, teat length, and teat diameter were examined at individual animal level and quarter level. Data were collected from the record register maintained at the farm and data evaluated by parity (no. of lactation) and stage of lactation. On analysis of variance, result revealed the significantly (P < 0.05) higher incidence of SCM was for pendulous shape udder in respect of regular udder, as well as for inverted and flat teat end shape in respect of pointed teat end shape. Large teat length and upper depth animals had significantly (P < 0.05) more incidence of SCM as compared to small and medium teat length and udder depth group, respectively. Thick teat diameter group animals were significantly (P < 0.01) more prone to infection as compared to medium and thin teat diameter group animals. So, it can be concluded that selection for optimum udder and teat morphometry in breeding program may help to reduce susceptibility for intramammary infections in Tharparkar cows. Microbiological study of milk samples could be helpful in the nearby future for identification of subclinical mastitis.

  19. Deformation-based brain morphometry in rats.

    PubMed

    Gaser, Christian; Schmidt, Silvio; Metzler, Martin; Herrmann, Karl-Heinz; Krumbein, Ines; Reichenbach, Jürgen R; Witte, Otto W

    2012-10-15

    Magnetic resonance imaging (MRI)-based morphometry provides in vivo evidence for macro-structural plasticity of the brain. Experiments on small animals using automated morphometric methods usually require expensive measurements with ultra-high field dedicated animal MRI systems. Here, we developed a novel deformation-based morphometry (DBM) tool for automated analyses of rat brain images measured on a 3-Tesla clinical whole body scanner with appropriate coils. A landmark-based transformation of our customized reference brain into the coordinates of the widely used rat brain atlas from Paxinos and Watson (Paxinos Atlas) guarantees the comparability of results to other studies. For cross-sectional data, we warped images onto the reference brain using the low-dimensional nonlinear registration implemented in the MATLAB software package SPM8. For the analysis of longitudinal data sets, we chose high-dimensional registrations of all images of one data set to the first baseline image which facilitate the identification of more subtle structural changes. Because all deformations were finally used to transform the data into the space of the Paxinos Atlas, Jacobian determinants could be used to estimate absolute local volumes of predefined regions-of-interest. Pilot experiments were performed to analyze brain structural changes due to aging or photothrombotically-induced cortical stroke. The results support the utility of DBM based on commonly available clinical whole-body scanners for highly sensitive morphometric studies on rats.

  20. Surface Polysaccharide Mutants Reveal that Absence of O Antigen Reduces Biofilm Formation of Actinobacillus pleuropneumoniae

    PubMed Central

    Hathroubi, S.; Hancock, M. A.; Langford, P. R.; Tremblay, Y. D. N.; Labrie, J.

    2015-01-01

    Actinobacillus pleuropneumoniae is a Gram-negative bacterium belonging to the Pasteurellaceae family and the causative agent of porcine pleuropneumonia, a highly contagious lung disease causing important economic losses. Surface polysaccharides, including lipopolysaccharides (LPS) and capsular polysaccharides (CPS), are implicated in the adhesion and virulence of A. pleuropneumoniae, but their role in biofilm formation is still unclear. In this study, we investigated the requirement for these surface polysaccharides in biofilm formation by A. pleuropneumoniae serotype 1. Well-characterized mutants were used: an O-antigen LPS mutant, a truncated core LPS mutant with an intact O antigen, a capsule mutant, and a poly-N-acetylglucosamine (PGA) mutant. We compared the amount of biofilm produced by the parental strain and the isogenic mutants using static and dynamic systems. Compared to the findings for the biofilm of the parental or other strains, the biofilm of the O antigen and the PGA mutants was dramatically reduced, and it had less cell-associated PGA. Real-time PCR analyses revealed a significant reduction in the level of pgaA, cpxR, and cpxA mRNA in the biofilm cells of the O-antigen mutant compared to that in the biofilm cells of the parental strain. Specific binding between PGA and LPS was consistently detected by surface plasmon resonance, but the lack of O antigen did not abolish these interactions. In conclusion, the absence of the O antigen reduces the ability of A. pleuropneumoniae to form a biofilm, and this is associated with the reduced expression and production of PGA. PMID:26483403

  1. Surface Polysaccharide Mutants Reveal that Absence of O Antigen Reduces Biofilm Formation of Actinobacillus pleuropneumoniae.

    PubMed

    Hathroubi, S; Hancock, M A; Bossé, J T; Langford, P R; Tremblay, Y D N; Labrie, J; Jacques, M

    2015-10-19

    Actinobacillus pleuropneumoniae is a Gram-negative bacterium belonging to the Pasteurellaceae family and the causative agent of porcine pleuropneumonia, a highly contagious lung disease causing important economic losses. Surface polysaccharides, including lipopolysaccharides (LPS) and capsular polysaccharides (CPS), are implicated in the adhesion and virulence of A. pleuropneumoniae, but their role in biofilm formation is still unclear. In this study, we investigated the requirement for these surface polysaccharides in biofilm formation by A. pleuropneumoniae serotype 1. Well-characterized mutants were used: an O-antigen LPS mutant, a truncated core LPS mutant with an intact O antigen, a capsule mutant, and a poly-N-acetylglucosamine (PGA) mutant. We compared the amount of biofilm produced by the parental strain and the isogenic mutants using static and dynamic systems. Compared to the findings for the biofilm of the parental or other strains, the biofilm of the O antigen and the PGA mutants was dramatically reduced, and it had less cell-associated PGA. Real-time PCR analyses revealed a significant reduction in the level of pgaA, cpxR, and cpxA mRNA in the biofilm cells of the O-antigen mutant compared to that in the biofilm cells of the parental strain. Specific binding between PGA and LPS was consistently detected by surface plasmon resonance, but the lack of O antigen did not abolish these interactions. In conclusion, the absence of the O antigen reduces the ability of A. pleuropneumoniae to form a biofilm, and this is associated with the reduced expression and production of PGA. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  2. Neuroanatomical Correlates of Developmental Dyscalculia: Combined Evidence from Morphometry and Tractography

    PubMed Central

    Rykhlevskaia, Elena; Uddin, Lucina Q.; Kondos, Leeza; Menon, Vinod

    2009-01-01

    Poor mathematical abilities adversely affect academic and career opportunities. The neuroanatomical basis of developmental dyscalculia (DD), a specific learning deficit with prevalence rates exceeding 5%, is poorly understood. We used structural MRI and diffusion tensor imaging (DTI) to examine macro- and micro-structural impairments in 7- to 9-year-old children with DD, compared to a group of typically developing (TD) children matched on age, gender, intelligence, reading abilities and working memory capacity. Voxel-based morphometry (VBM) revealed reduced grey matter (GM) bilaterally in superior parietal lobule, intra-parietal sulcus, fusiform gyrus, parahippocampal gyrus and right anterior temporal cortex in children with DD. VBM analysis also showed reduced white matter (WM) volume in right temporal-parietal cortex. DTI revealed reduced fractional anisotropy (FA) in this WM region, pointing to significant right hemisphere micro-structural impairments. Furthermore, FA in this region was correlated with numerical operations but not verbal mathematical reasoning or word reading. Atlas-based tract mapping identified the inferior longitudinal fasciculus, inferior fronto-occipital fasciculus and caudal forceps major as key pathways impaired in DD. DTI tractography suggests that long-range WM projection fibers linking the right fusiform gyrus with temporal-parietal WM are a specific source of vulnerability in DD. Network and classification analysis suggest that DD in children may be characterized by multiple dysfunctional circuits arising from a core WM deficit. Our findings link GM and WM abnormalities in children with DD and they point to macro- and micro-structural abnormalities in right hemisphere temporal-parietal WM, and pathways associated with it, as key neuroanatomical correlates of DD. PMID:20046827

  3. Examining population differences in cerebral morphometry between Chinese and Indian undergraduate students.

    PubMed

    Lu, Jieru; Peng, Bo; Saxena, Aditya; Zhou, Zhiyong; Zhou, Zhe; Zhang, Tao; Tong, Baotong; Wang, Suhong; Dai, Yakang

    2017-01-01

    The aim of this study is to examine potential population differences in brain morphometry using magnetic resonance imaging (MRI). Thirty-six Chinese and thirty-two Indian undergraduate students are included in this study. All images are processed using BrainLab toolbox to obtain the morphometric values of gray matter volume, cortical thickness, and cortical surface area in each region of interest (ROI). We use ROI-based analysis to investigate ethnic differences using the three types of measurements. Cerebral variations of the brain between Chinese and Indian groups are mostly distributed in the frontal lobe, temporal lobe, and occipital lobe. Subgroup analysis reveals sex differences between the two groups. Our study demonstrates population-related differences in brain morphometry (gray matter volume, cortical thickness, and cortical surface area) between Chinese and Indian undergraduates.

  4. Reproducibility in Nerve Morphometry: Comparison between Methods and among Observers

    PubMed Central

    Bilego Neto, Antônio Paulo da Costa; Silveira, Fernando Braga Cassiano; Rodrigues da Silva, Greice Anne; Sanada, Luciana Sayuri; Fazan, Valéria Paula Sassoli

    2013-01-01

    We investigated the reproducibility of a semiautomated method (computerized with manual intervention) for nerve morphometry (counting and measuring myelinated fibers) between three observers with different levels of expertise and experience with the method. Comparisons between automatic (fully computerized) and semiautomated morphometric methods performed by the same computer software using the same nerve images were also performed. Sural nerves of normal adult rats were used. Automatic and semiautomated morphometry of the myelinated fibers were made through the computer software KS-400. Semiautomated morphometry was conducted by three independent observers on the same images, using the semiautomated method. Automatic morphometry overestimated the myelin sheath area, thus overestimating the myelinated fiber size and underestimating the axon size. Fiber distributions overestimation was of 0.5 μm. For the semiautomated morphometry, no differences were found between observers for myelinated fiber and axon size distributions. Overestimation of the myelin sheath size of normal fibers by the fully automatic method might have an impact when morphometry is used for diagnostic purposes. We suggest that not only semiautomated morphometry results can be compared between different centers in clinical trials but it can also be performed by more than one investigator in one single experiment, being a reliable and reproducible method. PMID:23841086

  5. Declining streamflows reveal nonstationary orographic precipitation enhancement driven by reduced westerly flows

    NASA Astrophysics Data System (ADS)

    Luce, Charles; Abatzoglou, John; Holden, Zachary

    2016-04-01

    Although orographic enhancement of precipitation lends mountains an important role in water resources, they are dramatically undersampled by long-term precipitation gages. This has led to the widespread practice of extrapolating trends in low-elevation precipitation gage networks to high elevations via simple climatological precipitation ratios developed from isohyetal maps. An implicit assumption in such a process is non-stationarity in orographic precipitation enhancement, an assumption that can lead to large errors in trend detection and attribution of climate change effects. We show an example from the Northwestern United States where streamflows from mountain watersheds show substantial declines over the last 60 years, even while long-term precipitation gage networks in the region show no trend. We demonstrate that these observed streamflow declines are driven by previously unexplored differential trends in precipitation. November to March westerly winds are strongly correlated with high-elevation precipitation but weakly correlated with low-elevation precipitation. Decreases in winter westerlies across the region from 1950 to 2012 are hypothesized to have reduced orographic precipitation enhancement, yielding differential trends in precipitation across elevations leading to the apparent paradox. Climate projections show continued weakening meridional pressure gradients and westerly flow across the region under greenhouse forcing, highlighting an additional stressor that is relevant for climate change impacts on water resources. This study also reveals the potential of wind speed data from circulation reanalysis products to better inform historical precipitation reconstructions.

  6. Revealing, Reducing, and Representing Uncertainties in New Hydrologic Projections for Climate-changed Futures

    NASA Astrophysics Data System (ADS)

    Arnold, Jeffrey; Clark, Martyn; Gutmann, Ethan; Wood, Andy; Nijssen, Bart; Rasmussen, Roy

    2016-04-01

    The United States Army Corps of Engineers (USACE) has had primary responsibility for multi-purpose water resource operations on most of the major river systems in the U.S. for more than 200 years. In that time, the USACE projects and programs making up those operations have proved mostly robust against the range of natural climate variability encountered over their operating life spans. However, in some watersheds and for some variables, climate change now is known to be shifting the hydroclimatic baseline around which that natural variability occurs and changing the range of that variability as well. This makes historical stationarity an inappropriate basis for assessing continued project operations under climate-changed futures. That means new hydroclimatic projections are required at multiple scales to inform decisions about specific threats and impacts, and for possible adaptation responses to limit water-resource vulnerabilities and enhance operational resilience. However, projections of possible future hydroclimatologies have myriad complex uncertainties that require explicit guidance for interpreting and using them to inform those decisions about climate vulnerabilities and resilience. Moreover, many of these uncertainties overlap and interact. Recent work, for example, has shown the importance of assessing the uncertainties from multiple sources including: global model structure [Meehl et al., 2005; Knutti and Sedlacek, 2013]; internal climate variability [Deser et al., 2012; Kay et al., 2014]; climate downscaling methods [Gutmann et al., 2012; Mearns et al., 2013]; and hydrologic models [Addor et al., 2014; Vano et al., 2014; Mendoza et al., 2015]. Revealing, reducing, and representing these uncertainties is essential for defining the plausible quantitative climate change narratives required to inform water-resource decision-making. And to be useful, such quantitative narratives, or storylines, of climate change threats and hydrologic impacts must sample

  7. Modern morphometry: new perspectives in physical anthropology.

    PubMed

    Mantini, Simone; Ripani, Maurizio

    2009-06-01

    In the past one hundred years physical anthropology has recourse to more and more efficient methods, which provide several new information regarding, human evolution and biology. Apart from the molecular approach, the introduction of new computed assisted techniques gave rise to a new concept of morphometry. Computed tomography and 3D-imaging, allowed providing anatomical description of the external and inner structures exceeding the problems encountered with the traditional morphometric methods. Furthermore, the support of geometric morphometrics, allowed creating geometric models to investigate morphological variation in terms of evolution, ontogeny and variability. The integration of these new tools gave rise to the virtual anthropology and to a new image of the anthropologist in which anatomical, biological, mathematical statistical and data processing information are fused in a multidisciplinary approach.

  8. Reducing multi-sensor data to a single time course that reveals experimental effects

    PubMed Central

    2013-01-01

    Background Multi-sensor technologies such as EEG, MEG, and ECoG result in high-dimensional data sets. Given the high temporal resolution of such techniques, scientific questions very often focus on the time-course of an experimental effect. In many studies, researchers focus on a single sensor or the average over a subset of sensors covering a “region of interest” (ROI). However, single-sensor or ROI analyses ignore the fact that the spatial focus of activity is constantly changing, and fail to make full use of the information distributed over the sensor array. Methods We describe a technique that exploits the optimality and simplicity of matched spatial filters in order to reduce experimental effects in multivariate time series data to a single time course. Each (multi-sensor) time sample of each trial is replaced with its projection onto a spatial filter that is matched to an observed experimental effect, estimated from the remaining trials (Effect-Matched Spatial filtering, or EMS filtering). The resulting set of time courses (one per trial) can be used to reveal the temporal evolution of an experimental effect, which distinguishes this approach from techniques that reveal the temporal evolution of an anatomical source or region of interest. Results We illustrate the technique with data from a dual-task experiment and use it to track the temporal evolution of brain activity during the psychological refractory period. We demonstrate its effectiveness in separating the means of two experimental conditions, and in significantly improving the signal-to-noise ratio at the single-trial level. It is fast to compute and results in readily-interpretable time courses and topographies. The technique can be applied to any data-analysis question that can be posed independently at each sensor, and we provide one example, using linear regression, that highlights the versatility of the technique. Conclusion The approach described here combines established techniques in a

  9. Effects of cryopreservation on head morphometry and its relation with chromatin status in brown bear (Ursus arctos) spermatozoa.

    PubMed

    Alvarez, M; García-Macías, V; Martínez-Pastor, F; Martínez, F; Borragán, S; Mata, M; Garde, J; Anel, L; De Paz, P

    2008-12-01

    The Cantabrian brown bear (Ursus arctos) is a highly endangered species in Spain and basic studies are necessary in order to bank its germplasm. Sperm heads are mainly made up of chromatin, thus their shape depends partly on chromatin structure. Thawed semen from 10 bears was used to analyze chromatin status by sperm chromatin structure assay (SCSA) and head morphometry by the computer-assisted sperm morphology assessment (CASMA) system. Morphometry was analyzed before and after freezing-thawing in order to evaluate the effects of cryopreservation on sperm heads. Each spermatozoon was measured for four primary parameters (length, L; width, W; area, A; perimeter, P) and derived parameters (ellipticity: L/W, circularity: 4piA/ P2, elongation: (L-W)/(L+W), regularity: piLW/ 4A). All the derived parameters significantly differed between bears. Likewise, cryopreservation affected head morphometry by reducing its size. Clustering based on morphometric parameters separated three subpopulations, one of them being significantly more influenced by the cryopreservation process. We obtained high correlations between head morphometry and SCSA parameters: standard deviation of DNA fragmentation index (SD-DFI) was correlated with perimeter and area (r=0.75 and r=0.62, respectively) and DFIm and DFIt (moderate and total DNA fragmentation index) were correlated with perimeter (r=0.65 and r=0.67, respectively). Nevertheless, classification of males according to SCSA or head morphometry did not completely agree so the two assays might explain male variability differently. We conclude that cryopreservation affected morphometry at least in a subset of spermatozoa. These results might improve future application of sperm banking techniques in this species.

  10. Automated sperm morphometry analysis (ASMA) in the rabbit.

    PubMed

    Gravance, C G; Davis, R O

    1995-01-01

    New methods of specimen preparation were developed and a new method of objective, automated sperm morphometry analysis (ASMA) was performed to reduce the technical variation in the rabbit sperm morphology assay. The optimal staining procedure was a modified GZIN stain, which allowed the ASMA instrument to accurately recognize the distal end of the sperm head and to achieve the highest sperm recognition rate (94%). Washing and resuspending sperm to a standard concentration increased the number of sperm per microscopic field in low-concentration samples and reduced the field-to-field variation in all samples. Washing also decreased the number of sperm recognition errors by the ASMA instrument. Mean metric measurements for all sperm were: length, 7.38 microns; width, 3.91 microns; width/length, 0.53; area, 22.10 microns; and perimeter, 19.20 microns. Within-specimen coefficients of variation (CVs) ranged from 0.8% to 5.5% and between-animal CVs ranged from 2.7% to 7.5%. The use of standard specimen preparation techniques and ASMA technology can significantly reduce the technical variation in the rabbit sperm morphology assay.

  11. Blood-Gene Expression Reveals Reduced Circadian Rhythmicity in Individuals Resistant to Sleep Deprivation

    PubMed Central

    Arnardottir, Erna S.; Nikonova, Elena V.; Shockley, Keith R.; Podtelezhnikov, Alexei A.; Anafi, Ron C.; Tanis, Keith Q.; Maislin, Greg; Stone, David J.; Renger, John J.; Winrow, Christopher J.; Pack, Allan I.

    2014-01-01

    Study Objectives: To address whether changes in gene expression in blood cells with sleep loss are different in individuals resistant and sensitive to sleep deprivation. Design: Blood draws every 4 h during a 3-day study: 24-h normal baseline, 38 h of continuous wakefulness and subsequent recovery sleep, for a total of 19 time-points per subject, with every 2-h psychomotor vigilance task (PVT) assessment when awake. Setting: Sleep laboratory. Participants: Fourteen subjects who were previously identified as behaviorally resistant (n = 7) or sensitive (n = 7) to sleep deprivation by PVT. Intervention: Thirty-eight hours of continuous wakefulness. Measurements and Results: We found 4,481 unique genes with a significant 24-h diurnal rhythm during a normal sleep-wake cycle in blood (false discovery rate [FDR] < 5%). Biological pathways were enriched for biosynthetic processes during sleep. After accounting for circadian effects, two genes (SREBF1 and CPT1A, both involved in lipid metabolism) exhibited small, but significant, linear changes in expression with the duration of sleep deprivation (FDR < 5%). The main change with sleep deprivation was a reduction in the amplitude of the diurnal rhythm of expression of normally cycling probe sets. This reduction was noticeably higher in behaviorally resistant subjects than sensitive subjects, at any given P value. Furthermore, blood cell type enrichment analysis showed that the expression pattern difference between sensitive and resistant subjects is mainly found in cells of myeloid origin, such as monocytes. Conclusion: Individual differences in behavioral effects of sleep deprivation are associated with differences in diurnal amplitude of gene expression for genes that show circadian rhythmicity. Citation: Arnardottir ES, Nikonova EV, Shockley KR, Podtelezhnikov AA, Anafi RC, Tanis KQ, Maislin G, Stone DJ, Renger JJ, Winrow CJ, Pack AI. Blood-gene expression reveals reduced circadian rhythmicity in individuals resistant to

  12. Neuroanatomical phenotype of Klinefelter syndrome in childhood: a voxel-based morphometry study.

    PubMed

    Bryant, Daniel M; Hoeft, Fumiko; Lai, Song; Lackey, John; Roeltgen, David; Ross, Judith; Reiss, Allan L

    2011-05-04

    Klinefelter syndrome (KS) is a genetic disorder characterized by a supernumerary X chromosome. As such, KS offers a naturally occurring human model for the study of both X-chromosome gene expression and androgen on brain development. Previous neuroimaging studies have revealed neuroanatomical variations associated with KS, but have differed widely with respect to subject inclusion criteria, including mosaicism, pubertal status, and history of testosterone replacement therapy (TRT), all factors likely to influence neurodevelopment. We conducted a voxel-based morphometry study of regional gray and white matter (GM and WM, respectively) volumes in 31 KS males (mean age, 9.69 ± 1.70 years) and 36 typically developing (TD) male controls (10.99 ± 1.72 years). None of the participants with KS had received TRT, and all were prepubertal and had nonmosaic 47,XXY karyotypes. After controlling for age, males with KS showed trends (0.05 < p < 0.10) for significantly reduced total gray matter volume (TGMV) and total white matter volume (TWMV), relative to TD males. After controlling for TGMV and age, the KS group had significantly increased sensorimotor and parietal-occipital GM and significantly reduced amygdalar, hippocampal, insular, temporal, and inferior frontal GM relative to TD controls. After controlling for TWMV and age, the KS group had significantly increased left parietal WM as well as significantly reduced frontal and temporal WM. These findings are indicative of a characteristic prepubertal neuroanatomical phenotype that may be associated with cognitive-behavioral features of KS. This work offers new insight into the relationships among X-chromosome gene expression, neuroanatomy, and cognitive-behavioral functions impaired in KS, including language and attention.

  13. Volcano morphometry and volume scaling on Venus

    NASA Technical Reports Server (NTRS)

    Garvin, J. B.; Williams, R. S., Jr.

    1994-01-01

    A broad variety of volcanic edifices have been observed on Venus. They ranged in size from the limits of resolution of the Magellan SAR (i.e., hundreds of meters) to landforms over 500 km in basal diameter. One of the key questions pertaining to volcanism on Venus concerns the volume eruption rate or VER, which is linked to crustal productivity over time. While less than 3 percent of the surface area of Venus is manifested as discrete edifices larger than 50 km in diameter, a substantial component of the total crustal volume of the planet over the past 0.5 Ga is related to isolated volcanoes, which are certainly more easily studied than the relatively diffusely defined plains volcanic flow units. Thus, we have focused our efforts on constraining the volume productivity of major volcanic edifices larger than 100 km in basal diameter. Our approach takes advantage of the topographic data returned by Magellan, as well as our database of morphometric statistics for the 20 best known lava shields of Iceland, plus Mauna Loa of Hawaii. As part of this investigation, we have quantified the detailed morphometry of nearly 50 intermediate to large scale edifices, with particular attention to their shape systematics. We found that a set of venusian edifices which include Maat, Sapas, Tepev, Sif, Gula, a feature at 46 deg S, 215 deg E, as well as the shield-like structure at 10 deg N, 275 deg E are broadly representative of the approx. 400 volcanic landforms larger than 50 km. The cross-sectional shapes of these 7 representative edifices range from flattened cones (i.e., Sif) similar to classic terrestrial lava shields such as Mauna Loa and Skjaldbreidur, to rather dome-like structures which include Maat and Sapas. The majority of these larger volcanoes surveyed as part of our study displayed cross-sectional topographies with paraboloidal shaped, in sharp contrast with the cone-like appearance of most simple terrestrial lava shields. In order to more fully explore the

  14. Volcano morphometry and volume scaling on Venus

    NASA Astrophysics Data System (ADS)

    Garvin, J. B.; Williams, R. S., Jr.

    1994-03-01

    A broad variety of volcanic edifices have been observed on Venus. They ranged in size from the limits of resolution of the Magellan SAR (i.e., hundreds of meters) to landforms over 500 km in basal diameter. One of the key questions pertaining to volcanism on Venus concerns the volume eruption rate or VER, which is linked to crustal productivity over time. While less than 3 percent of the surface area of Venus is manifested as discrete edifices larger than 50 km in diameter, a substantial component of the total crustal volume of the planet over the past 0.5 Ga is related to isolated volcanoes, which are certainly more easily studied than the relatively diffusely defined plains volcanic flow units. Thus, we have focused our efforts on constraining the volume productivity of major volcanic edifices larger than 100 km in basal diameter. Our approach takes advantage of the topographic data returned by Magellan, as well as our database of morphometric statistics for the 20 best known lava shields of Iceland, plus Mauna Loa of Hawaii. As part of this investigation, we have quantified the detailed morphometry of nearly 50 intermediate to large scale edifices, with particular attention to their shape systematics. We found that a set of venusian edifices which include Maat, Sapas, Tepev, Sif, Gula, a feature at 46 deg S, 215 deg E, as well as the shield-like structure at 10 deg N, 275 deg E are broadly representative of the approx. 400 volcanic landforms larger than 50 km. The cross-sectional shapes of these 7 representative edifices range from flattened cones (i.e., Sif) similar to classic terrestrial lava shields such as Mauna Loa and Skjaldbreidur, to rather dome-like structures which include Maat and Sapas. The majority of these larger volcanoes surveyed as part of our study displayed cross-sectional topographies with paraboloidal shaped, in sharp contrast with the cone-like appearance of most simple terrestrial lava shields. In order to more fully explore the

  15. Analysis of RPE morphometry in human eyes

    PubMed Central

    Bhatia, Shagun K.; Rashid, Alia; Chrenek, Micah A.; Zhang, Qing; Bruce, Beau B.; Klein, Mitchel; Boatright, Jeffrey H.; Jiang, Yi; Grossniklaus, Hans E.

    2016-01-01

    Purpose To describe the RPE morphometry of healthy human eyes regarding age and topographic location using modern computational methods with high accuracy and objectivity. We tested whether there were regional and age-related differences in RPE cell area and shape. Methods Human cadaver donor eyes of varying ages were dissected, and the RPE flatmounts were immunostained for F-actin with AF635-phalloidin, nuclei stained with propidium iodide, and imaged with confocal microscopy. Image analysis was performed using ImageJ (NIH) and CellProfiler software. Quantitative parameters, including cell density, cell area, polygonality of cells, number of neighboring cells, and measures of cell shape, were obtained from these analyses to characterize individual and groups of RPE cells. Measurements were taken from selected areas spanning the length of the temporal retina through the macula and the mid-periphery to the far periphery. Results Nineteen eyes from 14 Caucasian donors of varying ages ranging from 29 to 80 years were used. Along a horizontal nasal to temporal meridian, there were differences in several cell shape and size characteristics. Generally, the cell area and shape was relatively constant and regular except in the far periphery. In the outer third of the retina, the cell area and shape differed from the inner two-thirds statistically significantly. In the macula and the far periphery, an overall decreasing trend in RPE cell density, percent hexagonal cells, and form factor was observed with increasing age. We also found a trend toward increasing cell area and eccentricity with age in the macula and the far periphery. When individuals were divided into two age groups, <60 years and ≥60 years, there was a higher cell density, lower cell area, lower eccentricity, and higher form factor in the younger group in the macula and the far periphery (p<0.05 for all measurements). No statistically significant differences in RPE morphometry between age groups were found

  16. Dog sperm head morphometry: its diversity and evolution.

    PubMed

    Soler, Carles; Alambiaga, Ana; Martí, Maria A; García-Molina, Almudena; Valverde, Anthony; Contell, Jesús; Campos, Marcos

    2017-01-01

    Dogs have been under strong artificial selection as a consequence of their relationship with man. Differences between breeds are evident that could be reflected in seminal characteristics. The present study was to evaluate differences in sperm head morphometry between seven well-defined breeds of dog: the British Bulldog, Chihuahua, German Shepherd, Labrador Retriever, Spanish Mastiff, Staffordshire Terrier, and Valencian Rat Hunting dog. Semen samples were obtained by masturbation and smears stained with Diff-Quik. Morphometric analysis (CASA-Morph) produced four size and four shape parameters. Length, Ellipticity, and Elongation showed higher differences between breeds. MANOVA revealed differences among all breeds. Considering the whole dataset, principal component analysis (PCA) showed that PC1 was related to head shape and PC2 to size. Procluster analysis showed the British Bulldog to be the most isolated breed, followed by the German Shepherd. The PCA breed by breed showed the Chihuahua, Labrador Retriever, Spanish Mastiff, and Staffordshire Terrier to have PC1 related to shape and PC2 to size, whereas the British Bulldog, Valencia Rat Hunting dog, and German Shepherd had PC1 related to size and PC2 to shape. The dendrogram for cluster groupings and the distance between them showed the British Bulldog to be separated from the rest of the breeds. Future work on dog semen must take into account the large differences in the breeds' sperm characteristics. The results provide a base for future work on phylogenetic and evolutionary studies of dogs, based on their seminal characteristics.

  17. Validation of voxel-based morphometry (VBM) based on MRI

    NASA Astrophysics Data System (ADS)

    Yang, Xueyu; Chen, Kewei; Guo, Xiaojuan; Yao, Li

    2007-03-01

    Voxel-based morphometry (VBM) is an automated and objective image analysis technique for detecting differences in regional concentration or volume of brain tissue composition based on structural magnetic resonance (MR) images. VBM has been used widely to evaluate brain morphometric differences between different populations, but there isn't an evaluation system for its validation until now. In this study, a quantitative and objective evaluation system was established in order to assess VBM performance. We recruited twenty normal volunteers (10 males and 10 females, age range 20-26 years, mean age 22.6 years). Firstly, several focal lesions (hippocampus, frontal lobe, anterior cingulate, back of hippocampus, back of anterior cingulate) were simulated in selected brain regions using real MRI data. Secondly, optimized VBM was performed to detect structural differences between groups. Thirdly, one-way ANOVA and post-hoc test were used to assess the accuracy and sensitivity of VBM analysis. The results revealed that VBM was a good detective tool in majority of brain regions, even in controversial brain region such as hippocampus in VBM study. Generally speaking, much more severity of focal lesion was, better VBM performance was. However size of focal lesion had little effects on VBM analysis.

  18. Dog sperm head morphometry: its diversity and evolution

    PubMed Central

    Soler, Carles; Alambiaga, Ana; Martí, Maria A; García-Molina, Almudena; Valverde, Anthony; Contell, Jesús; Campos, Marcos

    2017-01-01

    Dogs have been under strong artificial selection as a consequence of their relationship with man. Differences between breeds are evident that could be reflected in seminal characteristics. The present study was to evaluate differences in sperm head morphometry between seven well-defined breeds of dog: the British Bulldog, Chihuahua, German Shepherd, Labrador Retriever, Spanish Mastiff, Staffordshire Terrier, and Valencian Rat Hunting dog. Semen samples were obtained by masturbation and smears stained with Diff-Quik. Morphometric analysis (CASA-Morph) produced four size and four shape parameters. Length, Ellipticity, and Elongation showed higher differences between breeds. MANOVA revealed differences among all breeds. Considering the whole dataset, principal component analysis (PCA) showed that PC1 was related to head shape and PC2 to size. Procluster analysis showed the British Bulldog to be the most isolated breed, followed by the German Shepherd. The PCA breed by breed showed the Chihuahua, Labrador Retriever, Spanish Mastiff, and Staffordshire Terrier to have PC1 related to shape and PC2 to size, whereas the British Bulldog, Valencia Rat Hunting dog, and German Shepherd had PC1 related to size and PC2 to shape. The dendrogram for cluster groupings and the distance between them showed the British Bulldog to be separated from the rest of the breeds. Future work on dog semen must take into account the large differences in the breeds’ sperm characteristics. The results provide a base for future work on phylogenetic and evolutionary studies of dogs, based on their seminal characteristics. PMID:27751991

  19. Morphometry of Human Insular Cortex and Insular Volume Reduction in Williams syndrome

    PubMed Central

    Cohen, Jeremy D.; Mock, Jeffrey R.; Nichols, Taylor; Zadina, Janet; Corey, David M.; Lemen, Lisa; Bellugi, Ursula; Galaburda, Albert; Reiss, Allan; Foundas, Anne L.

    2009-01-01

    Functional imaging in humans and anatomical data in monkeys have implicated the insula as a multimodal sensory integrative brain region. The topography of insular connections is organized by its cytoarchitectonic regions. Previous attempts to measure the insula have utilized either indirect or automated methods. This study was designed to develop a reliable method for obtaining volumetric magnetic resonance imaging (MRI) measurements of the human insular cortex, and to validate that method by examining the anatomy of insular cortex in adults with Williams syndrome (WS) and healthy age-matched controls. Statistical reliability was obtained among three raters for this method, supporting its reproducibility not only across raters, but within different software packages. The procedure described here utilizes native-space morphometry as well as a method for dividing the insula into connectivity-based sub-regions estimated from cytoarchitectonics. Reliability was calculated in both ANALYZE (n=3) and BrainImageJava (N=10) where brain scans were measured once in each hemisphere by each rater. This highly reliable method revealed total, anterior, and posterior insular volume reduction bilaterally (all p’s < .002) in WS, after accounting for reduced total brain volumes in these participants. Although speculative, the reduced insular volumes in WS may represent a neural risk for the development of hyperaffiliative social behavior with increased specific phobias, and implicate the insula as a critical limbic integrative region. Native-space quantification of the insula may be valuable in the study of neurodevelopmental or neuropsychiatric disorders related to anxiety and social behavior. PMID:19660766

  20. Morphometry, geometry, function, and the future.

    PubMed

    Mcnulty, Kieran P; Vinyard, Christopher J

    2015-01-01

    The proliferation of geometric morphometrics (GM) in biological anthropology and more broadly throughout the biological sciences has resulted in a multitude of studies that adopt landmark-based approaches for addressing a variety of questions in evolutionary morphology. In some cases, particularly in the realm of systematics, the fit between research question and analytical design is quite good. Functional-adaptive studies, however, do not readily conform to the methods available in the GM toolkit. The symposium organized by Terhune and Cooke entitled "Assessing function via shape: What is the place of GM in functional morphology?" held at the 2013 meetings of the American Association of Physical Anthropologists was designed specifically to explore this relationship between landmark-based methods and analyses of functional morphology, and the articles in this special issue, which stem in large part from this symposium, provide numerous examples of how the two approaches can complement and contrast each other. Here, we underscore some of the major difficulties in interpreting GM results within a functional regime. In combination with other contributions in this issue, we identify emerging areas of research that will help bridge the gap between multivariate morphometry and functional-adaptive analysis. Ultimately, neither geometric nor functional morphometric approaches is sufficient to elaborate the adaptive pathways that explain morphological evolution through natural selection. These perspectives must be further integrated with research from physiology, developmental biology, genomics, and ecology. © 2014 Wiley Periodicals, Inc.

  1. A global database of composite volcano morphometry

    NASA Astrophysics Data System (ADS)

    Grosse, Pablo; Euillades, Pablo A.; Euillades, Leonardo D.; van Wyk de Vries, Benjamin

    2014-01-01

    We present a global database on the subaerial morphometry of composite volcanoes. Data was extracted from the 90-m resolution Shuttle Radar Topography Mission (SRTM) digital elevation model (DEM). The 759 volcanoes included in the database are the composite (i.e., polygenetic) volcanoes listed in the Smithsonian Institution Global Volcanism Program (GVP) database that are covered by the SRTM DEM, have a constructional topography and a basal width larger than 2 km. The extent of each volcano edifice was defined using the NETVOLC algorithm, which computes outlines by minimizing a cost function based on breaks in slope around the edifices. Morphometric parameters were then calculated using the MORVOLC algorithm. The parameters characterize and quantify volcano size (basal width, summit width, height, and volume), profile shape (height/basal width and summit width/basal width ratios), plan shape (ellipticity and irregularity indexes), and slopes. In addition, 104 well-defined and relatively large summit craters/calderas were manually delineated and specific parameters were computed. Most parameters show large variation without clear separations, indicating a continuum of volcano morphologies. Large overlap between the main GVP morphologic types highlights the need for a more rigorous quantitative classification of volcano morphology. The database will be maintained and updated through a website under construction.

  2. Puma (Puma concolor) epididymal sperm morphometry.

    PubMed

    Cucho, Hernán; Alarcón, Virgilio; Ordóñez, César; Ampuero, Enrique; Meza, Aydee; Soler, Carles

    2016-01-01

    The Andean puma (Puma concolor) has not been widely studied, particularly in reference to its semen characteristics. The aim of the present study was to define the morphometry of puma sperm heads and classify their subpopulations by cluster analysis. Samples were recovered postmortem from two epididymides from one animal and prepared for morphological observation after staining with the Hemacolor kit. Morphometric data were obtained from 581 spermatozoa using a CASA-Morph system, rendering 13 morphometric parameters. The principal component (PC) analysis was performed followed by cluster analysis for the establishment of subpopulations. Two PC components were obtained, the first related to size and the second to shape. Three subpopulations were observed, corresponding to elongated and intermediate-size sperm heads and acrosomes, to large heads with large acrosomes, and to small heads with short acrosomes. In conclusion, puma spermatozoa showed no uniform sperm morphology but three clear subpopulations. These results should be used for future work in the establishment of an adequate germplasm bank of this species.

  3. Puma (Puma concolor) epididymal sperm morphometry

    PubMed Central

    Cucho, Hernán; Alarcón, Virgilio; Ordóñez, César; Ampuero, Enrique; Meza, Aydee; Soler, Carles

    2016-01-01

    The Andean puma (Puma concolor) has not been widely studied, particularly in reference to its semen characteristics. The aim of the present study was to define the morphometry of puma sperm heads and classify their subpopulations by cluster analysis. Samples were recovered postmortem from two epididymides from one animal and prepared for morphological observation after staining with the Hemacolor kit. Morphometric data were obtained from 581 spermatozoa using a CASA-Morph system, rendering 13 morphometric parameters. The principal component (PC) analysis was performed followed by cluster analysis for the establishment of subpopulations. Two PC components were obtained, the first related to size and the second to shape. Three subpopulations were observed, corresponding to elongated and intermediate-size sperm heads and acrosomes, to large heads with large acrosomes, and to small heads with short acrosomes. In conclusion, puma spermatozoa showed no uniform sperm morphology but three clear subpopulations. These results should be used for future work in the establishment of an adequate germplasm bank of this species. PMID:27678466

  4. Morphometry in pathology: another look at diagnostic histopathology.

    PubMed

    Collan, Y

    1984-11-01

    Histopathology is crucial for diagnostic and therapeutic decisions in many disease states. The created classifications, however, have not always allowed explicit recognition of diagnostic categories. So, considerable intra- and interobserver variations are possible under diagnostic circumstances. Better reproducibility can be reached by applying other than traditional methods. These include morphometry as well as special stains, electron microscopy and immunohistochemistry. Morphometry is basic in that in detects structural and morphological aberrations in samples prepared by other methods and without doubt brings the element of accuracy to support the diagnostic decision. Morphometric approach includes item classification and grading, point counting and intersection counting methods, and the use of various semiautomatic or automatic instruments. In statistical morphometry morphometrical parameters are collected from several disease cases. Such data reinforced with prognostic follow-ups are the basis for disease classification. Diagnostic morphometry, on the other hand, tries to study the sample of one individual and give relevant data for diagnostic decisions. Morphometric methods allow estimation of the limits of possible performance in histopathology, estimation of human performance in the diagnostic process and estimation of the influence of interfering human factors. Diagnostic decisions as well as decisions linked with therapy are basically probabilistic. Also the data collected by diagnostic morphometry should be linked with probabilistic estimates of the prognostic relevance of the findings. Education of histopathology should be developed to meet these demands, both at elementary medical level and at postgraduate medical level. Education of morphometry can be incorporated into the medical curricula as shown by the experience at the University of Kuopio where aspects of morphometry are taught during histopathology course and special postgraduate courses have

  5. Stem transcriptome reveals mechanisms to reduce the energetic cost of shade-avoidance responses in tomato.

    PubMed

    Cagnola, Juan Ignacio; Ploschuk, Edmundo; Benech-Arnold, Tomás; Finlayson, Scott A; Casal, Jorge José

    2012-10-01

    While the most conspicuous response to low red/far-red ratios (R:FR) of shade light perceived by phytochrome is the promotion of stem growth, additional, less obvious effects may be discovered by studying changes in the stem transcriptome. Here, we report rapid and reversible stem transcriptome responses to R:FR in tomato (Solanum lycopersicum). As expected, low R:FR promoted the expression of growth-related genes, including those involved in the metabolism of cell wall carbohydrates and in auxin responses. In addition, genes involved in flavonoid synthesis, isoprenoid metabolism, and photosynthesis (dark reactions) were overrepresented in clusters showing reduced expression in the stem of low R:FR-treated plants. Consistent with these responses, low R:FR decreased the levels of flavonoids (anthocyanin, quercetin, kaempferol) and selected isoprenoid derivatives (chlorophyll, carotenoids) in the stem and severely reduced the photosynthetic capacity of this organ. However, lignin contents were unaffected. Low R:FR reduced the stem levels of jasmonate, which is a known inducer of flavonoid synthesis. The rate of stem respiration was also reduced in low R:FR-treated plants, indicating that by downsizing the stem photosynthetic apparatus and the levels of photoprotective pigments under low R:FR, tomato plants reduce the energetic cost of shade-avoidance responses.

  6. Reduced representation bisulphite sequencing of the ten bovine somatic tissues reveals DNA methylation patterns

    USDA-ARS?s Scientific Manuscript database

    As a major component epigenetics, DNA methylation has been proved that widely functions in individual development and various diseases. It has been well studied in model organisms and human but includes limited data for the economic animals. Using reduced representation bisulphite sequencing (RRBS),...

  7. Reduced representation bisulphite sequencing of the cattle genome reveals DNA methylation patterns

    USDA-ARS?s Scientific Manuscript database

    Using reduced representation bisulphite sequencing (RRBS), we obtained the first single-base-resolution maps of bovine DNA methylation in ten somatic tissues. In total, we observed 1,868,049 cytosines in the CG-enriched regions. Similar to the methylation patterns in other species, the CG context wa...

  8. On the morphometry of terrestrial shield volcanoes

    NASA Astrophysics Data System (ADS)

    Grosse, Pablo; Kervyn, Matthieu

    2016-04-01

    Shield volcanoes are described as low angle edifices that have convex up topographic profiles and are built primarily by the accumulation of lava flows. This generic view of shields' morphology is based on a limited number of monogenetic shields from Iceland and Mexico, and a small set of large oceanic islands (Hawaii, Galapagos). Here, the morphometry of over 150 monogenetic and polygenetic shield volcanoes, identified inthe Global Volcanism Network database, are analysed quantitatively from 90-meter resolution DEMs using the MORVOLC algorithm. An additional set of 20 volcanoes identified as stratovolcanoes but having low slopes and being dominantly built up by accumulation of lava flows are documented for comparison. Results show that there is a large variation in shield size (volumes range from 0.1 to >1000 km3), profile shape (height/basal width ratios range from 0.01 to 0.1), flank slope gradients, elongation and summit truncation. Correlation and principal component analysis of the obtained quantitative database enables to identify 4 key morphometric descriptors: size, steepness, plan shape and truncation. Using these descriptors through clustering analysis, a new classification scheme is proposed. It highlights the control of the magma feeding system - either central, along a linear structure, or spatially diffuse - on the resulting shield volcano morphology. Genetic relationships and evolutionary trends between contrasted morphological end-members can be highlighted within this new scheme. Additional findings are that the Galapagos-type morphology with a central deep caldera and steep upper flanks are characteristic of other shields. A series of large oceanic shields have slopes systematically much steeper than the low gradients (<4-8°) generally attributed to large Hawaiian-type shields. Finally, the continuum of morphologies from flat shields to steeper complex volcanic constructs considered as stratovolcanoes calls for a revision of this oversimplified

  9. Effects of two different probiotics on microflora, morphology, and morphometry of gut in organic laying hens.

    PubMed

    Forte, C; Acuti, G; Manuali, E; Casagrande Proietti, P; Pavone, S; Trabalza-Marinucci, M; Moscati, L; Onofri, A; Lorenzetti, C; Franciosini, M P

    2016-11-01

    The current study investigated the effects of Lactobacillus acidophilus and Bacillus subtilis, used as probiotics, on the microflora, morphology, and morphometry of the gut in organic laying hens. The birds (180 Hy-Line laying hens) were divided into 3 homogenous groups and received a pre-deposition diet from 16 to 20 wk of age and a deposition diet for the remaining 7 months of the experiment. The control group ( CTR: ) was fed a corn-soybean cake-based diet, the second group ( L: ) received the same diet supplemented with 0.1% of L. acidophilus while in the third group ( B: ) the basal diet was supplemented with 0.05% of B. subtilis At 18 wk of age ( T1: ) and at 5 ( T2: ) and 7 months ( T3: ) from the beginning of deposition, 9 subjects per group were humanely killed for microbiological, morphological and morphometric analyses of the intestinal tract. The 2 probiotic-supplemented diets increased Lactobacillus spp. and Bifidobacterium spp. counts compared with the CTR diet. The lowest viable counts of E. coli, coliforms and staphylococci were observed in the L group (P < 0.001). Clostridium spp. decreased (P < 0.001) in both L and B subjects. The probiotic supplementation appeared to affect the intestinal microbial population, promoting the presence of beneficial bacteria such as Lactobacillus spp. and Bifidobacterium spp. and reducing potential harmful bacteria such as E. coli, clostridia and staphylococci. Morphological and morphometric analyses did not reveal substantial differences among groups. At T3, the plasma cell infiltrate in the villi of the CTR hens was more severe than that observed in the L and B groups (P = 0.009).

  10. So Near and Yet So Far: Harmonic Radar Reveals Reduced Homing Ability of Nosema Infected Honeybees

    PubMed Central

    Wolf, Stephan; McMahon, Dino P.; Lim, Ka S.; Pull, Christopher D.; Clark, Suzanne J.; Paxton, Robert J.; Osborne, Juliet L.

    2014-01-01

    Pathogens may gain a fitness advantage through manipulation of the behaviour of their hosts. Likewise, host behavioural changes can be a defence mechanism, counteracting the impact of pathogens on host fitness. We apply harmonic radar technology to characterize the impact of an emerging pathogen - Nosema ceranae (Microsporidia) - on honeybee (Apis mellifera) flight and orientation performance in the field. Honeybees are the most important commercial pollinators. Emerging diseases have been proposed to play a prominent role in colony decline, partly through sub-lethal behavioural manipulation of their hosts. We found that homing success was significantly reduced in diseased (65.8%) versus healthy foragers (92.5%). Although lost bees had significantly reduced continuous flight times and prolonged resting times, other flight characteristics and navigational abilities showed no significant difference between infected and non-infected bees. Our results suggest that infected bees express normal flight characteristics but are constrained in their homing ability, potentially compromising the colony by reducing its resource inputs, but also counteracting the intra-colony spread of infection. We provide the first high-resolution analysis of sub-lethal effects of an emerging disease on insect flight behaviour. The potential causes and the implications for both host and parasite are discussed. PMID:25098331

  11. So near and yet so far: harmonic radar reveals reduced homing ability of Nosema infected honeybees.

    PubMed

    Wolf, Stephan; McMahon, Dino P; Lim, Ka S; Pull, Christopher D; Clark, Suzanne J; Paxton, Robert J; Osborne, Juliet L

    2014-01-01

    Pathogens may gain a fitness advantage through manipulation of the behaviour of their hosts. Likewise, host behavioural changes can be a defence mechanism, counteracting the impact of pathogens on host fitness. We apply harmonic radar technology to characterize the impact of an emerging pathogen--Nosema ceranae (Microsporidia)--on honeybee (Apis mellifera) flight and orientation performance in the field. Honeybees are the most important commercial pollinators. Emerging diseases have been proposed to play a prominent role in colony decline, partly through sub-lethal behavioural manipulation of their hosts. We found that homing success was significantly reduced in diseased (65.8%) versus healthy foragers (92.5%). Although lost bees had significantly reduced continuous flight times and prolonged resting times, other flight characteristics and navigational abilities showed no significant difference between infected and non-infected bees. Our results suggest that infected bees express normal flight characteristics but are constrained in their homing ability, potentially compromising the colony by reducing its resource inputs, but also counteracting the intra-colony spread of infection. We provide the first high-resolution analysis of sub-lethal effects of an emerging disease on insect flight behaviour. The potential causes and the implications for both host and parasite are discussed.

  12. Multiple electron transfer systems in oxygen reducing biocathodes revealed by different conditions of aeration/agitation.

    PubMed

    Rimboud, Mickaël; Bergel, Alain; Erable, Benjamin

    2016-08-01

    Oxygen reducing biocathodes were formed at -0.2V/SCE (+0.04V/SHE) from compost leachate. Depending on whether aeration was implemented or not, two different redox systems responsible for the electrocatalysis of oxygen reduction were evidenced. System I was observed at low potential (-0.03V/SHE) on cyclic voltammetries (CVs). It appeared during the early formation of the biocathode (few hours) and resisted the hydrodynamic conditions induced by the aeration. System II was observed at higher potential on CV (+0.46V/SHE); it required a longer lag time (up to 10days) and quiescent conditions to produce an electrochemical signal. The hydrodynamic effects produced by the forced aeration led to its extinction. From their different behaviors and examples in the literature, system I was identified as being a membrane-bound cytochrome-related molecule, while system II was identified as a soluble redox mediator excreted by the biofilm. This study highlighted the importance of controlling the local hydrodynamics to design efficient oxygen reducing biocathodes able to operate at high potential.

  13. Lake Morphometry for NHD Lakes in California Region 18 HUC

    EPA Pesticide Factsheets

    Lake morphometry metrics are known to influence productivity in lakes and are important for building various types of ecological and environmental models of lentic systems. The lake morphometry dataset included here contains estimates of Surface Area, Shoreline Length, Shoreline Development, Maximum Depth, Mean Depth, Lake Volume, Maximum Lake Length, Mean Lake Width, Maximum Lake Width, and Fetch for each of the ??lakepond?? waterbodies in the NHDPlus V2. The current release of the datasets is version 0.1 and future refinements to the data are expected.

  14. Lake Morphometry for NHD Lakes in Tennessee Region 6 HUC

    EPA Pesticide Factsheets

    Lake morphometry metrics are known to influence productivity in lakes and are important for building various types of ecological and environmental models of lentic systems. The lake morphometry dataset included here contains estimates of Surface Area, Shoreline Length, Shoreline Development, Maximum Depth, Mean Depth, Lake Volume, Maximum Lake Length, Mean Lake Width, Maximum Lake Width, and Fetch for each of the ??lakepond?? waterbodies in the NHDPlus V2. The current release of the datasets is version 0.1 and future refinements to the data are expected.

  15. Lake Morphometry for NHD Lakes in Ohio Region 5 HUC

    EPA Pesticide Factsheets

    Lake morphometry metrics are known to influence productivity in lakes and are important for building various types of ecological and environmental models of lentic systems. The lake morphometry dataset included here contains estimates of Surface Area, Shoreline Length, Shoreline Development, Maximum Depth, Mean Depth, Lake Volume, Maximum Lake Length, Mean Lake Width, Maximum Lake Width, and Fetch for each of the ??lakepond?? waterbodies in the NHDPlus V2. The current release of the datasets is version 0.1 and future refinements to the data are expected.

  16. Buried iceberg scours reveal reduced North Atlantic Current during the stage 12 deglacial

    NASA Astrophysics Data System (ADS)

    Newton, Andrew M. W.; Huuse, Mads; Brocklehurst, Simon H.

    2016-03-01

    Reconstructing past ocean-climate environments and heat transport requires proxies from which these conditions can be quantified. This is particularly important for the evaluation of numerical palaeoclimate models. Here we present new evidence for a reduced North Atlantic Current (NAC) at the termination of the third last glacial, for which palaeocurrent information was previously unavailable. This is based on an exquisitely preserved set of buried iceberg scours seen in three-dimensional seismic reflection images from the mid-Norwegian slope. The scours were formed ~430 ka during the transition from glacial to interglacial conditions. The spiral geometry of the scours suggests that they were carved by grounded icebergs influenced by tidal and geostrophic ocean currents. Using the ratio between the estimated tidal and geostrophic current velocities and comparing them with velocities from the Last Glacial Maximum and the present, we show that the stage 12 NAC velocities may have been ~50% slower than the present.

  17. Buried iceberg scours reveal reduced North Atlantic Current during the stage 12 deglacial

    PubMed Central

    Newton, Andrew M. W.; Huuse, Mads; Brocklehurst, Simon H.

    2016-01-01

    Reconstructing past ocean-climate environments and heat transport requires proxies from which these conditions can be quantified. This is particularly important for the evaluation of numerical palaeoclimate models. Here we present new evidence for a reduced North Atlantic Current (NAC) at the termination of the third last glacial, for which palaeocurrent information was previously unavailable. This is based on an exquisitely preserved set of buried iceberg scours seen in three-dimensional seismic reflection images from the mid-Norwegian slope. The scours were formed ∼430 ka during the transition from glacial to interglacial conditions. The spiral geometry of the scours suggests that they were carved by grounded icebergs influenced by tidal and geostrophic ocean currents. Using the ratio between the estimated tidal and geostrophic current velocities and comparing them with velocities from the Last Glacial Maximum and the present, we show that the stage 12 NAC velocities may have been ∼50% slower than the present. PMID:26979836

  18. Metagenomics Reveals Pervasive Bacterial Populations and Reduced Community Diversity across the Alaska Tundra Ecosystem

    SciTech Connect

    Johnston, Eric R.; Rodriguez-R, Luis M.; Luo, Chengwei; Yuan, Mengting M.; Wu, Liyou; He, Zhili; Schuur, Edward A. G.; Luo, Yiqi; Tiedje, James M.; Zhou, Jizhong; Konstantinidis, Konstantinos T.

    2016-04-25

    How soil microbial communities contrast with respect to taxonomic and functional composition within and between ecosystems remains an unresolved question that is central to predicting how global anthropogenic change will affect soil functioning and services. In particular, it remains unclear how small-scale observations of soil communities based on the typical volume sampled (1-2 g) are generalizable to ecosystem-scale responses and processes. This is especially relevant for remote, northern latitude soils, which are challenging to sample and are also thought to be more vulnerable to climate change compared to temperate soils. Here, we employed well-replicated shotgun metagenome and 16S rRNA gene amplicon sequencing to characterize community composition and metabolic potential in Alaskan tundra soils, combining our own datasets with those publically available from distant tundra and temperate grassland and agriculture habitats. We found that the abundance of many taxa and metabolic functions differed substantially between tundra soil metagenomes relative to those from temperate soils, and that a high degree of OTU-sharing exists between tundra locations. Tundra soils were an order of magnitude less complex than their temperate counterparts, allowing for near-complete coverage of microbial community richness (~92% breadth) by sequencing, and the recovery of 27 high-quality, almost complete ( > 80% completeness) population bins. These population bins, collectively, made up to ~10% of the metagenomic datasets, and represented diverse taxonomic groups and metabolic lifestyles tuned toward sulfur cycling, hydrogen metabolism, methanotrophy, and organic matter oxidation. Several population bins, including members of Acidobacteria, Actinobacteria, and Proteobacteria, were also present in geographically distant (~100-530 km apart) tundra habitats (full genome representation and up to 99.6% genome-derived average nucleotide identity). Collectively, our results revealed that

  19. Metagenomics Reveals Pervasive Bacterial Populations and Reduced Community Diversity across the Alaska Tundra Ecosystem.

    PubMed

    Johnston, Eric R; Rodriguez-R, Luis M; Luo, Chengwei; Yuan, Mengting M; Wu, Liyou; He, Zhili; Schuur, Edward A G; Luo, Yiqi; Tiedje, James M; Zhou, Jizhong; Konstantinidis, Konstantinos T

    2016-01-01

    How soil microbial communities contrast with respect to taxonomic and functional composition within and between ecosystems remains an unresolved question that is central to predicting how global anthropogenic change will affect soil functioning and services. In particular, it remains unclear how small-scale observations of soil communities based on the typical volume sampled (1-2 g) are generalizable to ecosystem-scale responses and processes. This is especially relevant for remote, northern latitude soils, which are challenging to sample and are also thought to be more vulnerable to climate change compared to temperate soils. Here, we employed well-replicated shotgun metagenome and 16S rRNA gene amplicon sequencing to characterize community composition and metabolic potential in Alaskan tundra soils, combining our own datasets with those publically available from distant tundra and temperate grassland and agriculture habitats. We found that the abundance of many taxa and metabolic functions differed substantially between tundra soil metagenomes relative to those from temperate soils, and that a high degree of OTU-sharing exists between tundra locations. Tundra soils were an order of magnitude less complex than their temperate counterparts, allowing for near-complete coverage of microbial community richness (~92% breadth) by sequencing, and the recovery of 27 high-quality, almost complete (>80% completeness) population bins. These population bins, collectively, made up to ~10% of the metagenomic datasets, and represented diverse taxonomic groups and metabolic lifestyles tuned toward sulfur cycling, hydrogen metabolism, methanotrophy, and organic matter oxidation. Several population bins, including members of Acidobacteria, Actinobacteria, and Proteobacteria, were also present in geographically distant (~100-530 km apart) tundra habitats (full genome representation and up to 99.6% genome-derived average nucleotide identity). Collectively, our results revealed that

  20. Rice Domestication Revealed by Reduced Shattering of Archaeological rice from the Lower Yangtze valley

    PubMed Central

    Zheng, Yunfei; Crawford, Gary W.; Jiang, Leping; Chen, Xugao

    2016-01-01

    Plant remains dating to between 9000 and 8400 BP from a probable ditch structure at the Huxi site include the oldest rice (Oryza sativa) spikelet bases and associated plant remains recovered in China. The remains document an early stage of rice domestication and the ecological setting in which early cultivation was taking place. The rice spikelet bases from Huxi include wild (shattering), intermediate, and domesticated (non-shattering) forms. The relative frequency of intermediate and non-shattering spikelet bases indicates that selection for, at the very least, non-shattering rice was underway at Huxi. The rice also has characteristics of japonica rice (Oryza sativa subsp. japonica), helping to clarify the emergence of a significant lineage of the crop. Seeds, phytoliths and their context provide evidence of increasing anthropogenesis and cultivation during the occupation. Rice spikelet bases from Kuahuqiao (8000–7700 BP), Tianluoshan (7000–6500 BP), Majiabang (6300–6000 BP), and Liangzhu (5300–4300 BP) sites indicate that rice underwent continuing selection for reduced shattering and japonica rice characteristics, confirming a prolonged domestication process for rice. PMID:27324699

  1. Comparative selenoproteome analysis reveals a reduced utilization of selenium in parasitic platyhelminthes.

    PubMed

    Jiang, Liang; Zhu, Hua-Zhang; Xu, Yin-Zhen; Ni, Jia-Zuan; Zhang, Yan; Liu, Qiong

    2013-01-01

    Background. The selenocysteine(Sec)-containing proteins, selenoproteins, are an important group of proteins present in all three kingdoms of life. Although the selenoproteomes of many organisms have been analyzed, systematic studies on selenoproteins in platyhelminthes are still lacking. Moreover, comparison of selenoproteomes between free-living and parasitic animals is rarely studied. Results. In this study, three representative organisms (Schmidtea mediterranea, Schistosoma japonicum and Taenia solium) were selected for comparative analysis of selenoproteomes in Platyhelminthes. Using a SelGenAmic-based selenoprotein prediction algorithm, a total of 37 selenoprotein genes were identified in these organisms. The size of selenoproteomes and selenoprotein families were found to be associated with different lifestyles: free-living organisms have larger selenoproteome whereas parasitic lifestyle corresponds to reduced selenoproteomes. Five selenoproteins, SelT, Sel15, GPx, SPS2 and TR, were found to be present in all examined platyhelminthes as well as almost all sequenced animals, suggesting their essential role in metazoans. Finally, a new splicing form of SelW that lacked the first exon was found to be present in S. japonicum. Conclusions. Our data provide a first glance into the selenoproteomes of organisms in the phylum Platyhelminthes and may help understand function and evolutionary dynamics of selenium utilization in diversified metazoans.

  2. Comparative selenoproteome analysis reveals a reduced utilization of selenium in parasitic platyhelminthes

    PubMed Central

    Jiang, Liang; Zhu, Hua-Zhang; Xu, Yin-Zhen; Ni, Jia-Zuan

    2013-01-01

    Background. The selenocysteine(Sec)-containing proteins, selenoproteins, are an important group of proteins present in all three kingdoms of life. Although the selenoproteomes of many organisms have been analyzed, systematic studies on selenoproteins in platyhelminthes are still lacking. Moreover, comparison of selenoproteomes between free-living and parasitic animals is rarely studied. Results. In this study, three representative organisms (Schmidtea mediterranea, Schistosoma japonicum and Taenia solium) were selected for comparative analysis of selenoproteomes in Platyhelminthes. Using a SelGenAmic-based selenoprotein prediction algorithm, a total of 37 selenoprotein genes were identified in these organisms. The size of selenoproteomes and selenoprotein families were found to be associated with different lifestyles: free-living organisms have larger selenoproteome whereas parasitic lifestyle corresponds to reduced selenoproteomes. Five selenoproteins, SelT, Sel15, GPx, SPS2 and TR, were found to be present in all examined platyhelminthes as well as almost all sequenced animals, suggesting their essential role in metazoans. Finally, a new splicing form of SelW that lacked the first exon was found to be present in S. japonicum. Conclusions. Our data provide a first glance into the selenoproteomes of organisms in the phylum Platyhelminthes and may help understand function and evolutionary dynamics of selenium utilization in diversified metazoans. PMID:24255816

  3. Reduced corpus callosum white matter microstructural integrity revealed by diffusion tensor eigenvalues in abstinent methamphetamine addicts.

    PubMed

    Kim, In-Sung; Kim, Yang-Tae; Song, Hui-Jin; Lee, Jae-Jun; Kwon, Do-Hoon; Lee, Hui Joong; Kim, Myoung-Nam; Yoo, Done-Sik; Chang, Yongmin

    2009-03-01

    The purpose of the current study was to determine whether abstinent methamphetamine (MA) abusers demonstrate differences in white matter (WM) integrity of the corpus callosum (CC) due to possible neurotoxic effects of long-term MA abuse, compared with control subjects. In addition to fractional anisotropy (FA), the eigenvalues of the diffusion ellipsoid were used to evaluate the microstructural source of abnormal change in abstinent MA abusers if there occurred a difference in white matter integrity of the CC between healthy controls and abstinent MA abusers. Results showed significantly reduced FA in the genu of the corpus callosum in MA-dependent subjects compared with controls. Furthermore, the eigenvalues offered a unique opportunity to assess the microstructural source of abnormal changes in the genu of the CC. The relationships between Wisconsin Card Sorting Test (WCST) performance and the values of tensor measures also suggest that altered myelination is a possible source of FA reduction observed in the genu of the CC in MA abusers.

  4. Annotation of the Asian Citrus Psyllid Genome Reveals a Reduced Innate Immune System

    PubMed Central

    Arp, Alex P.; Hunter, Wayne B.; Pelz-Stelinski, Kirsten S.

    2016-01-01

    Citrus production worldwide is currently facing significant losses due to citrus greening disease, also known as Huanglongbing. The citrus greening bacteria, Candidatus Liberibacter asiaticus (CLas), is a persistent propagative pathogen transmitted by the Asian citrus psyllid, Diaphorina citri Kuwayama (Hemiptera: Liviidae). Hemipterans characterized to date lack a number of insect immune genes, including those associated with the Imd pathway targeting Gram-negative bacteria. The D. citri draft genome was used to characterize the immune defense genes present in D. citri. Predicted mRNAs identified by screening the published D. citri annotated draft genome were manually searched using a custom database of immune genes from previously annotated insect genomes. Toll and JAK/STAT pathways, general defense genes Dual oxidase, Nitric oxide synthase, prophenoloxidase, and cellular immune defense genes were present in D. citri. In contrast, D. citri lacked genes for the Imd pathway, most antimicrobial peptides, 1,3-β-glucan recognition proteins (GNBPs), and complete peptidoglycan recognition proteins. These data suggest that D. citri has a reduced immune capability similar to that observed in A. pisum, P. humanus, and R. prolixus. The absence of immune system genes from the D. citri genome may facilitate CLas infections, and is possibly compensated for by their relationship with their microbial endosymbionts. PMID:27965582

  5. Annotation of the Asian Citrus Psyllid Genome Reveals a Reduced Innate Immune System.

    PubMed

    Arp, Alex P; Hunter, Wayne B; Pelz-Stelinski, Kirsten S

    2016-01-01

    Citrus production worldwide is currently facing significant losses due to citrus greening disease, also known as Huanglongbing. The citrus greening bacteria, Candidatus Liberibacter asiaticus (CLas), is a persistent propagative pathogen transmitted by the Asian citrus psyllid, Diaphorina citri Kuwayama (Hemiptera: Liviidae). Hemipterans characterized to date lack a number of insect immune genes, including those associated with the Imd pathway targeting Gram-negative bacteria. The D. citri draft genome was used to characterize the immune defense genes present in D. citri. Predicted mRNAs identified by screening the published D. citri annotated draft genome were manually searched using a custom database of immune genes from previously annotated insect genomes. Toll and JAK/STAT pathways, general defense genes Dual oxidase, Nitric oxide synthase, prophenoloxidase, and cellular immune defense genes were present in D. citri. In contrast, D. citri lacked genes for the Imd pathway, most antimicrobial peptides, 1,3-β-glucan recognition proteins (GNBPs), and complete peptidoglycan recognition proteins. These data suggest that D. citri has a reduced immune capability similar to that observed in A. pisum, P. humanus, and R. prolixus. The absence of immune system genes from the D. citri genome may facilitate CLas infections, and is possibly compensated for by their relationship with their microbial endosymbionts.

  6. DNA Elements Reducing Transcriptional Gene Silencing Revealed by a Novel Screening Strategy

    PubMed Central

    Ueno, Keiichiro; Ohashi, Yuko; Mitsuhara, Ichiro

    2013-01-01

    Transcriptional gene silencing (TGS)–a phenomenon observed in endogenous genes/transgenes in eukaryotes–is a huge hindrance to transgenic technology and occurs mainly when the genes involved share sequence homology in their promoter regions. TGS depends on chromosomal position, suggesting the existence of genomic elements that suppress TGS. However, no systematic approach to identify such DNA elements has yet been reported. Here, we developed a successful novel screening strategy to identify such elements (anti-silencing regions–ASRs), based on their ability to protect a flanked transgene from TGS. A silenced transgenic tobacco plant in which a subsequently introduced transgene undergoes obligatory promoter-homology dependent TGS in trans allowed the ability of DNA elements to prevent TGS to be used as the screening criterion. We also identified ASRs in a genomic library from a different plant species (Lotus japonicus: a perennial legume); the ASRs include portions of Ty1/copia retrotransposon-like and pararetrovirus-like sequences; the retrotransposon-like sequences also showed interspecies anti-TGS activity in a TGS-induction system in Arabidopsis. Anti-TGS elements could provide effective tools to reduce TGS and ensure proper regulation of transgene expression. Furthermore, the screening strategy described here will also facilitate the efficient identification of new classes of anti-TGS elements. PMID:23382937

  7. Rice Domestication Revealed by Reduced Shattering of Archaeological rice from the Lower Yangtze valley

    NASA Astrophysics Data System (ADS)

    Zheng, Yunfei; Crawford, Gary W.; Jiang, Leping; Chen, Xugao

    2016-06-01

    Plant remains dating to between 9000 and 8400 BP from a probable ditch structure at the Huxi site include the oldest rice (Oryza sativa) spikelet bases and associated plant remains recovered in China. The remains document an early stage of rice domestication and the ecological setting in which early cultivation was taking place. The rice spikelet bases from Huxi include wild (shattering), intermediate, and domesticated (non-shattering) forms. The relative frequency of intermediate and non-shattering spikelet bases indicates that selection for, at the very least, non-shattering rice was underway at Huxi. The rice also has characteristics of japonica rice (Oryza sativa subsp. japonica), helping to clarify the emergence of a significant lineage of the crop. Seeds, phytoliths and their context provide evidence of increasing anthropogenesis and cultivation during the occupation. Rice spikelet bases from Kuahuqiao (8000-7700 BP), Tianluoshan (7000-6500 BP), Majiabang (6300-6000 BP), and Liangzhu (5300-4300 BP) sites indicate that rice underwent continuing selection for reduced shattering and japonica rice characteristics, confirming a prolonged domestication process for rice.

  8. Metagenomics Reveals Pervasive Bacterial Populations and Reduced Community Diversity across the Alaska Tundra Ecosystem

    PubMed Central

    Johnston, Eric R.; Rodriguez-R, Luis M.; Luo, Chengwei; Yuan, Mengting M.; Wu, Liyou; He, Zhili; Schuur, Edward A. G.; Luo, Yiqi; Tiedje, James M.; Zhou, Jizhong; Konstantinidis, Konstantinos T.

    2016-01-01

    How soil microbial communities contrast with respect to taxonomic and functional composition within and between ecosystems remains an unresolved question that is central to predicting how global anthropogenic change will affect soil functioning and services. In particular, it remains unclear how small-scale observations of soil communities based on the typical volume sampled (1–2 g) are generalizable to ecosystem-scale responses and processes. This is especially relevant for remote, northern latitude soils, which are challenging to sample and are also thought to be more vulnerable to climate change compared to temperate soils. Here, we employed well-replicated shotgun metagenome and 16S rRNA gene amplicon sequencing to characterize community composition and metabolic potential in Alaskan tundra soils, combining our own datasets with those publically available from distant tundra and temperate grassland and agriculture habitats. We found that the abundance of many taxa and metabolic functions differed substantially between tundra soil metagenomes relative to those from temperate soils, and that a high degree of OTU-sharing exists between tundra locations. Tundra soils were an order of magnitude less complex than their temperate counterparts, allowing for near-complete coverage of microbial community richness (~92% breadth) by sequencing, and the recovery of 27 high-quality, almost complete (>80% completeness) population bins. These population bins, collectively, made up to ~10% of the metagenomic datasets, and represented diverse taxonomic groups and metabolic lifestyles tuned toward sulfur cycling, hydrogen metabolism, methanotrophy, and organic matter oxidation. Several population bins, including members of Acidobacteria, Actinobacteria, and Proteobacteria, were also present in geographically distant (~100–530 km apart) tundra habitats (full genome representation and up to 99.6% genome-derived average nucleotide identity). Collectively, our results revealed

  9. Metagenomics Reveals Pervasive Bacterial Populations and Reduced Community Diversity across the Alaska Tundra Ecosystem

    DOE PAGES

    Johnston, Eric R.; Rodriguez-R, Luis M.; Luo, Chengwei; ...

    2016-04-25

    revealed that Alaska tundra microbial communities are less diverse and more homogenous across spatial scales than previously anticipated, and provided DNA sequences of abundant populations and genes that would be relevant for future studies of the effects of environmental change on tundra ecosystems.« less

  10. Evolution of the insect body plan as revealed by the Sex combs reduced expression pattern.

    PubMed

    Rogers, B T; Peterson, M D; Kaufman, T C

    1997-01-01

    The products of the HOM/Hox homeotic genes form a set of evolutionarily conserved transcription factors that control elaborate developmental processes and specify cell fates in many metazoans. We examined the expression of the ortholog of the homeotic gene Sex combs reduced (Scr) of Drosophila melanogaster in insects of three divergent orders: Hemiptera, Orthoptera and Thysanura. Our data reflect how the conservation and variation of Scr expression has affected the morphological evolution of insects. Whereas the anterior epidermal expression of Scr, in a small part of the posterior maxillary and all of the labial segment, is found to be in common among all four insect orders, the posterior (thoracic) expression domains vary. Unlike what is observed in flies, the Scr orthologs of other insects are not expressed broadly over the first thoracic segment, but are restricted to small patches. We show here that Scr is required for suppression of wings on the prothorax of Drosophila. Moreover, Scr expression at the dorsal base of the prothoracic limb in two other winged insects, crickets (Orthoptera) and milkweed bugs (Hemiptera), is consistent with Scr acting as a suppressor of prothoracic wings in these insects. Scr is also expressed in a small patch of cells near the basitarsal-tibial junction of milkweed bugs, precisely where a leg comb develops, suggesting that Scr promotes comb formation, as it does in Drosophila. Surprisingly, the dorsal prothoracic expression of Scr is also present in the primitively wingless firebrat (Thysanura) and the leg patch is seen in crickets, which have no comb. Mapping both gene expression patterns and morphological characters onto the insect phylogenetic tree demonstrates that in the cases of wing suppression and comb formation the appearance of expression of Scr in the prothorax apparently precedes these specific functions.

  11. Central Tropical Pacific Corals Reveal Reduced ENSO Variability 3-5kyBP

    NASA Astrophysics Data System (ADS)

    Grothe, P. R.; Cobb, K. M.; Liguori, G.; Edwards, R. L.; Cheng, H.; Deocampo, D.; Southon, J. R.; Santos, G.; Lu, Y.; Capotondi, A.; Di Lorenzo, E.

    2015-12-01

    Future projections of the strength of the El Niño-Southern Oscillation (ENSO), the largest source of year-to-year global climate extremes, are highly uncertain. Potential shifts towards stronger and more frequent ENSO extremes (Cai et al., 2014; Kim et al., 2015) would have a profound effect on climate globally. However, the instrumental record of ENSO activity is too short in time to resolve potential anthropogenic trends in ENSO properties, and limits our understanding of the ENSO phenomenon. Thus, we must rely on high-resolution paleoclimate reconstructions of ENSO that extend through the last centuries to millennia to provide a comprehensive view of ENSO variability. Coral δ18O records from the heart of the ENSO region, in the central tropical Pacific, provide monthly-resolved reconstructions of ENSO activity over the last 7000 years. Here, we quantify ENSO variability in 10 new monthly-resolved fossil coral δ18O records from Kiritimati Island (2°N, 157°W) that are U/Th-dated to the 2-6kyBP interval. When combined with previously published coral δ18O records from Cobb et al., 2013, the new coral δ18O records support a prolonged reduction of ~60% in ENSO variability during the 3-5kyBP interval, as compared to the late 20th century. In comparison, ENSO variability during the last millennium was ~30% reduced compared to the late 20th century. These results are consistent with foraminifera and mollusk records from the eastern tropical Pacific (Koutavas and Joanides, 2012; Carre et al., 2014), implying that the observed 3-5kyBP reduction in ENSO variability was not confined to the central Pacific. Taken together, these new records represent a new target - both in terms of amplitude and timing - for modeling efforts designed to uncover the mechanisms governing past ENSO variability. Such data-model comparisons are critical to refining the simulation of ENSO in simulations of future climate change.

  12. Quantitative morphometry of glomerulonephritis with crescents. Diagnostic and predictive value.

    PubMed

    Elfenbein, I B; Baluarte, H J; Cubillos-Rojas, M; Gruskin, A B; Coté, M; Cornfeld, D

    1975-01-01

    Histologic patterns in the glomerular tufts in "Glomerulonephritis with many crescents" take three main forms: (1) compression and sclerosis of glomeruli, (2) necrotizing glomerulitis, and (3) proliferation with or without exudation. In the third group, histologic differentiation between patients with poststreptococcal glomerulonephritis with many crescents (AGN) and those with nonstreptococcal rapidly progressive glomerulonephritis (RPGN) may be impossible. In a retrospective study, quantitative morphometry of glomeruli effectively separated three patients with AGN from two patients with RPGN after the usual histologic and electron microscopic observations had failed. Parameters studied were areas of tufts and crescents and total number of cells and granulocytes in tufts and crescents. Surface areas of tufts and crescents were separately determined by photographing glomeruli, projecting and tracing outlines of tufts and crescents, and cutting out and weighing the tracings. The cell density of glomerular tufts (cell per 1000-sq. mum. area) was significantly greater in AGN than in RPGN when either total cell densities (17.64 plus or minus 0.41 versus 13.63 plus or minus 0.30) or total cells minus granulocytes (16.39 plus or minus 0.50 versus 12.99 plus or minus 0.52) were compared. The cell density in the tufts was 120 and 70 per cent greater than controls in AGN and RPGN, respectively. Exudation of inflammatory cells is contributory but not the major cause of hypercellularity in AGN. Follow-up studies with biopsies showed marked resolution in two of three patients with AGN, with normal blood urea nitrogen levels and focal scarring in the third, whereas the two patients with RPGN had either extensive scarring and reduced renal function or required chronic hemodialysis.

  13. Conformal invariants for multiply connected surfaces: Application to landmark curve-based brain morphometry analysis.

    PubMed

    Shi, Jie; Zhang, Wen; Tang, Miao; Caselli, Richard J; Wang, Yalin

    2017-01-01

    Landmark curves were widely adopted in neuroimaging research for surface correspondence computation and quantified morphometry analysis. However, most of the landmark based morphometry studies only focused on landmark curve shape difference. Here we propose to compute a set of conformal invariant-based shape indices, which are associated with the landmark curve induced boundary lengths in the hyperbolic parameter domain. Such shape indices may be used to identify which surfaces are conformally equivalent and further quantitatively measure surface deformation. With the surface Ricci flow method, we can conformally map a multiply connected surface to the Poincaré disk. Our algorithm provides a stable method to compute the shape index values in the 2D (Poincaré Disk) parameter domain. The proposed shape indices are succinct, intrinsic and informative. Experimental results with synthetic data and 3D MRI data demonstrate that our method is invariant under isometric transformations and able to detect brain surface abnormalities. We also applied the new shape indices to analyze brain morphometry abnormalities associated with Alzheimer' s disease (AD). We studied the baseline MRI scans of a set of healthy control and AD patients from the Alzheimer' s Disease Neuroimaging Initiative (ADNI: 30 healthy control subjects vs. 30 AD patients). Although the lengths of the landmarks in Euclidean space, cortical surface area, and volume features did not differ between the two groups, our conformal invariant based shape indices revealed significant differences by Hotelling' s T(2) test. The novel conformal invariant shape indices may offer a new sensitive biomarker and enrich our brain imaging analysis toolset for studying diagnosis and prognosis of AD. Copyright © 2016 Elsevier B.V. All rights reserved.

  14. Morfometryka and the search for constraints on galaxy morphometry

    NASA Astrophysics Data System (ADS)

    Ferreira, Leonardo; Ferrari, Fabricio

    2016-03-01

    Morfometryka is a standalone python application that makes photometry and morphometry a easy task. It is designed to be used in large datasets. By combining Morfometryka and Machine Learning we are able to reproduce human classification using only a small set of independent features that actually have physical meaning.

  15. Computer-assisted sperm morphometry fluorescence-based analysis has potential to determine progeny sex

    PubMed Central

    Santolaria, Pilar; Pauciullo, Alfredo; Silvestre, Miguel A; Vicente-Fiel, Sandra; Villanova, Leyre; Pinton, Alain; Viruel, Juan; Sales, Ester; Yániz, Jesús L

    2016-01-01

    This study was designed to determine the ability of computer-assisted sperm morphometry analysis (CASA-Morph) with fluorescence to discriminate between spermatozoa carrying different sex chromosomes from the nuclear morphometrics generated and different statistical procedures in the bovine species. The study was divided into two experiments. The first was to study the morphometric differences between X- and Y-chromosome-bearing spermatozoa (SX and SY, respectively). Spermatozoa from eight bulls were processed to assess simultaneously the sex chromosome by FISH and sperm morphometry by fluorescence-based CASA-Morph. SX cells were larger than SY cells on average (P < 0.001) although with important differences between bulls. A simultaneous evaluation of all the measured features by discriminant analysis revealed that nuclear area and average fluorescence intensity were the variables selected by stepwise discriminant function analysis as the best discriminators between SX and SY. In the second experiment, the sperm nuclear morphometric results from CASA-Morph in nonsexed (mixed SX and SY) and sexed (SX) semen samples from four bulls were compared. FISH allowed a successful classification of spermatozoa according to their sex chromosome content. X-sexed spermatozoa displayed a larger size and fluorescence intensity than nonsexed spermatozoa (P < 0.05). We conclude that the CASA-Morph fluorescence-based method has the potential to find differences between X- and Y-chromosome-bearing spermatozoa in bovine species although more studies are needed to increase the precision of sex determination by this technique. PMID:27624989

  16. Computer-assisted sperm morphometry fluorescence-based analysis has potential to determine progeny sex.

    PubMed

    Santolaria, Pilar; Pauciullo, Alfredo; Silvestre, Miguel A; Vicente-Fiel, Sandra; Villanova, Leyre; Pinton, Alain; Viruel, Juan; Sales, Ester; Yániz, Jesús L

    2016-01-01

    This study was designed to determine the ability of computer-assisted sperm morphometry analysis (CASA-Morph) with fluorescence to discriminate between spermatozoa carrying different sex chromosomes from the nuclear morphometrics generated and different statistical procedures in the bovine species. The study was divided into two experiments. The first was to study the morphometric differences between X- and Y-chromosome-bearing spermatozoa (SX and SY, respectively). Spermatozoa from eight bulls were processed to assess simultaneously the sex chromosome by FISH and sperm morphometry by fluorescence-based CASA-Morph. SX cells were larger than SY cells on average (P < 0.001) although with important differences between bulls. A simultaneous evaluation of all the measured features by discriminant analysis revealed that nuclear area and average fluorescence intensity were the variables selected by stepwise discriminant function analysis as the best discriminators between SX and SY. In the second experiment, the sperm nuclear morphometric results from CASA-Morph in nonsexed (mixed SX and SY) and sexed (SX) semen samples from four bulls were compared. FISH allowed a successful classification of spermatozoa according to their sex chromosome content. X-sexed spermatozoa displayed a larger size and fluorescence intensity than nonsexed spermatozoa (P < 0.05). We conclude that the CASA-Morph fluorescence-based method has the potential to find differences between X- and Y-chromosome-bearing spermatozoa in bovine species although more studies are needed to increase the precision of sex determination by this technique.

  17. Comparative structural morphometry and elemental composition of three marine sponges from western coast of India.

    PubMed

    Kumar, Maushmi S; Shah, Bhaumik

    2014-04-01

    Three marine sponges Halichondria glabrata, Cliono lobata, and Spirastrella pachyspira from the western coastal region of India were compared for their morphometry, biochemical, and elemental composition. One-way analysis of variance was applied for spicule morphometry results. Length, width, and length:width ratio were calculated independently. The ratio of length:width varied from 35 to 42 among the grown samples, which remained in the range of 10-22 in young sample at the beginning of studies. However, no significant change was observed in spicule width compared to length. Elemental compositions of marine sponges were determined by field emission gun-scanning electron microscope. Scanning electron microscopy data revealed that the spicules of all the three sponges were mostly composed of O (47-56%) and Si (30-40%), whereas Al (14.33%) was only detected in the spicules of C. lobata. Apart from these, K, Ni, Ca, Fe, Mg, Na, and S were additionally detected in all the three samples. Presence of heavy metals in the sponges was analyzed by inductively coupled plasma-atomic emission spectroscopy. Results showed that iron was present in a large amount in samples, followed by zinc, lead, and copper. Copyright © 2014 Wiley Periodicals, Inc.

  18. Pathology and morphometry of Hystrichis acanthocephalicus (Nematoda) from Phimosus infuscatus (Pelecaniformes) in southern Brazil.

    PubMed

    Scheer, Simone; Macedo, Márcia Raquel Pegoraro; Soares, Mauro Pereira; Schramm, Camila Costa; Muller, Gertrud

    2017-01-26

    Species of Hystrichis are parasite nematodes of the digestive tract of aquatic birds in South America, Europe and Asia. In Brazil, Hystrichis acanthocephalicus has been reported in Phimosus infuscatus. There are few data on the morphometry of this species and there are no reports on pathological conditions that it causes. Therefore, the purpose of this study was to report morphometric data from H. acanthocephalicus and describe the pathological effects of this parasite on the Phimosus infuscatus proventriculus. Thirty gastrointestinal tracts of P. infuscatus were examined to search for nematodes and H. acanthocephalicus occurred in 83% of hosts. Were measured the total length and body width of males and females, and of their respective cuticular spines, esophagus, spicules and eggs, and the internal and external diameter of copulatory bursa. Histopathological examination revealed parasitic structures in the proventriculus from the lumen (anterior end) to the outer layers of the organ (intermediate and posterior parts), in which we observed inflammatory reaction with infiltration of heterophils, hemorrhage and hemosiderin. The results of this study of histopathology, morphometry and parasitological indices are the first ones reported to H. acanthocephalicus and should contribute to the identification and recognition in cases of outbreaks in the Neotropical region.

  19. Structural covariance in the hallucinating brain: a voxel-based morphometry study

    PubMed Central

    Modinos, Gemma; Vercammen, Ans; Mechelli, Andrea; Knegtering, Henderikus; McGuire, Philip K.; Aleman, André

    2009-01-01

    Background Neuroimaging studies have indicated that a number of cortical regions express altered patterns of structural covariance in schizophrenia. The relation between these alterations and specific psychotic symptoms is yet to be investigated. We used voxel-based morphometry to examine regional grey matter volumes and structural covariance associated with severity of auditory verbal hallucinations. Methods We applied optimized voxel-based morphometry to volumetric magnetic resonance imaging data from 26 patients with medication-resistant auditory verbal hallucinations (AVHs); statistical inferences were made at p < 0.05 after correction for multiple comparisons. Results Grey matter volume in the left inferior frontal gyrus was positively correlated with severity of AVHs. Hallucination severity influenced the pattern of structural covariance between this region and the left superior/middle temporal gyri, the right inferior frontal gyrus and hippocampus, and the insula bilaterally. Limitations The results are based on self-reported severity of auditory hallucinations. Complementing with a clinician-based instrument could have made the findings more compelling. Future studies would benefit from including a measure to control for other symptoms that may covary with AVHs and for the effects of antipsychotic medication. Conclusion The results revealed that overall severity of AVHs modulated cortical intercorrelations between frontotemporal regions involved in language production and verbal monitoring, supporting the critical role of this network in the pathophysiology of hallucinations. PMID:19949723

  20. Reducing contralateral SI activity reveals hindlimb receptive fields in the SI forelimb-stump representation of neonatally amputated rats.

    PubMed

    Pluto, Charles P; Chiaia, Nicolas L; Rhoades, Robert W; Lane, Richard D

    2005-09-01

    In adult rats that sustained forelimb amputation on the day of birth, >30% of multiunit recording sites in the forelimb-stump representation of primary somatosensory cortex (SI) also respond to cutaneous hindlimb stimulation when cortical GABA(A+B) receptors are blocked (GRB). This study examined whether hindlimb receptive fields could also be revealed in forelimb-stump sites by reducing one known source of excitatory input to SI GABAergic neurons, the contralateral SI cortex. Corpus callosum projection neurons connect homotopic SI regions, making excitatory contacts onto pyramidal cells and interneurons. Thus in addition to providing monosynaptic excitation in SI, callosal fibers can produce disynaptic inhibition through excitatory synapses with inhibitory interneurons. Based on the latter of these connections, we hypothesized that inactivating the contralateral (intact) SI forelimb region would "unmask" normally suppressed hindlimb responses by reducing the activity of SI GABAergic neurons. The SI forelimb-stump representation was first mapped under normal conditions and then during GRB to identify stump/hindlimb responsive sites. After GRB had dissipated, the contralateral (intact) SI forelimb region was mapped and reversibly inactivated with injections of 4% lidocaine, and selected forelimb-stump sites were retested. Contralateral SI inactivation revealed hindlimb responses in approximately 60% of sites that were stump/hindlimb responsive during GRB. These findings indicate that activity in the contralateral SI contributes to the suppression of reorganized hindlimb receptive fields in neonatally amputated rats.

  1. Magnetic resonance morphometry of the loss of gray matter volume in Parkinson's disease patients

    PubMed Central

    Xia, Jianguo; Wang, Juan; Tian, Weizhong; Ding, Hongbin; Wei, Qilin; Huang, Huanxin; Wang, Jun; Zhao, Jinli; Gu, Hongmei; Tang, Lemin

    2013-01-01

    Voxel-based morphometry can be used to quantitatively compare structural differences and func-tional changes of gray matter in subjects. In the present study, we compared gray matter images of 32 patients with Parkinson's disease and 25 healthy controls using voxel-based morphometry based on 3.0 T high-field magnetic resonance T1-weighted imaging and clinical neurological scale scores. Results showed that the scores in Mini-Mental State Examination and Montreal Cognitive Assessment were lower in patients compared with controls. In particular, the scores of visuospa-tial/executive function items in Montreal Cognitive Assessment were significantly reduced, but mean scores of non-motor symptoms significantly increased, in patients with Parkinson's disease. In dition, gray matter volume was significantly diminished in Parkinson's disease patients compared with normal controls, including bilateral temporal lobe, bilateral occipital lobe, bilateral parietal lobe, bilateral frontal lobe, bilateral insular lobe, bilateral parahippocampal gyrus, bilateral amygdale, right uncus, and right posterior lobe of the cerebellum. These findings indicate that voxel-based phometry can accurately and quantitatively assess the loss of gray matter volume in patients with Parkinson' disease, and provide essential neuroimaging evidence for multisystem pathological mechanisms involved in Parkinson's disease. PMID:25206566

  2. [Voxel-Based Morphometry in Autism Spectrum Disorder].

    PubMed

    Yamasue, Hidenori

    2017-05-01

    Autism spectrum disorder shows deficits in social communication and interaction including nonverbal communicative behaviors (e.g., eye contact, gestures, voice prosody, and facial expressions) and restricted and repetitive behaviors as its core symptoms. These core symptoms are emerged as an atypical behavioral development in toddlers with the disorder. Atypical neural development is considered to be a neural underpinning of such behaviorally atypical development. A number of studies using voxel-based morphometry have already been conducted to compare regional brain volumes between individuals with autism spectrum disorder and those with typical development. Furthermore, more than ten papers employing meta-analyses of the comparisons using voxel based morphometry between individuals with autism spectrum disorder and those with typical development have already been published. The current review paper adds some brief discussions about potential factors contributing to the inconsistency observed in the previous findings such as difficulty in controlling the confounding effects of different developmental phases among study participants.

  3. The study of Lake Urmia desiccation: morphometry impress

    NASA Astrophysics Data System (ADS)

    Moradi, Ayoub; Rasouli, Ali Akbar; Roostaei, Shahram

    2017-04-01

    Located in northwestern Iran, the hypersaline Lake Urmia has started a serious uninterrupted desiccation since 1995. The lake has lost about eight meters of water level and about 75% of water surface area during past 20 years. In particular, the lake water volume decrement has been accelerated in recent years. The importance of the Lake Urmia for human life in northwestern Iran, and its destructive effects on a vast region if totally dry up, demands comprehensive studies of the lake level fluctuations mechanism. According to literature review, the water volume of the lake behaves sometimes differently from the water storage of the whole basin. Our time series analysis using Land Data Assimilation Systems also confirms those differences within last decades. In other hand, many studies addressed the lake desiccation to climatic changes and/or anthropogenic influences such as excessive dam constructions in the watershed during last decades. As water leaves the lake only through evaporation, the fluctuation of evaporation has a distinctive role in the lake level variations. Dramatic decreament in the lake extent indicates of a special morphometry. The lake's morphometry has made it vulnerable to temperature and salinity changes. It strongly controls the lake's water heat capacity and water density. And, it therefore controls the rate of evaporation from water surface. We study the role of lake's morphometry on the lake desiccation. Although, the global climatic change is known as the primary reason for current droughts in the Middle East generally, our preliminary results show that the lake's morphometry is the main cause for the accelerating of water volume lost in Lake Urmia. In particular, after 2007, lake's water temperature and density show significant variations. Water heat capacity and evaporation rate are consistent with information of lake's hypsometry.

  4. DNA fragmentation and sperm head morphometry in cat epididymal spermatozoa.

    PubMed

    Vernocchi, Valentina; Morselli, Maria Giorgia; Lange Consiglio, Anna; Faustini, Massimo; Luvoni, Gaia Cecilia

    2014-10-15

    Sperm DNA fragmentation is an important parameter to assess sperm quality and can be a putative fertility predictor. Because the sperm head consists almost entirely of DNA, subtle differences in sperm head morphometry might be related to DNA status. Several techniques are available to analyze sperm DNA fragmentation, but they are labor-intensive and require expensive instrumentations. Recently, a kit (Sperm-Halomax) based on the sperm chromatin dispersion test and developed for spermatozoa of different species, but not for cat spermatozoa, became commercially available. The first aim of the present study was to verify the suitability of Sperm-Halomax assay, specifically developed for canine semen, for the evaluation of DNA fragmentation of epididymal cat spermatozoa. For this purpose, DNA fragmentation indexes (DFIs) obtained with Sperm-Halomax and terminal deoxynucleotidyl transferase-mediated nick-end labeling (TUNEL) were compared. The second aim was to investigate whether a correlation between DNA status, sperm head morphology, and morphometry assessed by computer-assisted semen analysis exists in cat epididymal spermatozoa. No differences were observed in DFIs obtained with Sperm-Halomax and TUNEL. This result indicates that Sperm-Halomax assay provides a reliable evaluation of DNA fragmentation of epididymal feline spermatozoa. The DFI seems to be independent from all the measured variables of sperm head morphology and morphometry. Thus, the evaluation of the DNA status of spermatozoa could effectively contribute to the completion of the standard analysis of fresh or frozen semen used in assisted reproductive technologies.

  5. Metabolic Characterization of Intact Cells Reveals Intracellular Amyloid Beta but Not Its Precursor Protein to Reduce Mitochondrial Respiration.

    PubMed

    Schaefer, Patrick M; von Einem, Bjoern; Walther, Paul; Calzia, Enrico; von Arnim, Christine A F

    2016-01-01

    One hallmark of Alzheimer´s disease are senile plaques consisting of amyloid beta (Aβ), which derives from the processing of the amyloid precursor protein (APP). Mitochondrial dysfunction has been linked to the pathogenesis of Alzheimer´s disease and both Aβ and APP have been reported to affect mitochondrial function in isolated systems. However, in intact cells, considering a physiological localization of APP and Aβ, it is pending what triggers the mitochondrial defect. Thus, the aim of this study was to dissect the impact of APP versus Aβ in inducing mitochondrial alterations with respect to their subcellular localization. We performed an overexpression of APP or beta-site amyloid precursor protein cleaving enzyme 1 (BACE1), increasing APP and Aβ levels or Aβ alone, respectively. Conducting a comprehensive metabolic characterization we demonstrate that only APP overexpression reduced mitochondrial respiration, despite lower extracellular Aβ levels compared to BACE overexpression. Surprisingly, this could be rescued by a gamma secretase inhibitor, oppositionally indicating an Aβ-mediated mitochondrial toxicity. Analyzing Aβ localization revealed that intracellular levels of Aβ and an increased spatial association of APP/Aβ with mitochondria are associated with reduced mitochondrial respiration. Thus, our data provide marked evidence for a prominent role of intracellular Aβ accumulation in Alzheimer´s disease associated mitochondrial dysfunction. Thereby it highlights the importance of the localization of APP processing and intracellular transport as a decisive factor for mitochondrial function, linking two prominent hallmarks of neurodegenerative diseases.

  6. Metabolic Characterization of Intact Cells Reveals Intracellular Amyloid Beta but Not Its Precursor Protein to Reduce Mitochondrial Respiration

    PubMed Central

    Schaefer, Patrick M.; von Einem, Bjoern; Walther, Paul; Calzia, Enrico; von Arnim, Christine A. F.

    2016-01-01

    One hallmark of Alzheimer´s disease are senile plaques consisting of amyloid beta (Aβ), which derives from the processing of the amyloid precursor protein (APP). Mitochondrial dysfunction has been linked to the pathogenesis of Alzheimer´s disease and both Aβ and APP have been reported to affect mitochondrial function in isolated systems. However, in intact cells, considering a physiological localization of APP and Aβ, it is pending what triggers the mitochondrial defect. Thus, the aim of this study was to dissect the impact of APP versus Aβ in inducing mitochondrial alterations with respect to their subcellular localization. We performed an overexpression of APP or beta-site amyloid precursor protein cleaving enzyme 1 (BACE1), increasing APP and Aβ levels or Aβ alone, respectively. Conducting a comprehensive metabolic characterization we demonstrate that only APP overexpression reduced mitochondrial respiration, despite lower extracellular Aβ levels compared to BACE overexpression. Surprisingly, this could be rescued by a gamma secretase inhibitor, oppositionally indicating an Aβ-mediated mitochondrial toxicity. Analyzing Aβ localization revealed that intracellular levels of Aβ and an increased spatial association of APP/Aβ with mitochondria are associated with reduced mitochondrial respiration. Thus, our data provide marked evidence for a prominent role of intracellular Aβ accumulation in Alzheimer´s disease associated mitochondrial dysfunction. Thereby it highlights the importance of the localization of APP processing and intracellular transport as a decisive factor for mitochondrial function, linking two prominent hallmarks of neurodegenerative diseases. PMID:28005987

  7. Escherichia coli K-12 pathogenicity in the pea aphid, Acyrthosiphon pisum, reveals reduced antibacterial defense in aphids.

    PubMed

    Altincicek, Boran; Ter Braak, Bas; Laughton, Alice M; Udekwu, Klas I; Gerardo, Nicole M

    2011-10-01

    To better understand the molecular basis underlying aphid immune tolerance to beneficial bacteria and immune defense to pathogenic bacteria, we characterized how the pea aphid Acyrthosiphon pisum responds to Escherichia coli K-12 infections. E. coli bacteria, usually cleared in the hemolymph of other insect species, were capable of growing exponentially and killing aphids within a few days. Red fluorescence protein expressing E. coli K-12 laboratory strain multiplied in the aphid hemolymph as well as in the digestive tract, resulting in death of infected aphids. Selected gene deletion mutants of the E. coli K-12 predicted to have reduced virulence during systemic infections showed no difference in either replication or killing rate when compared to the wild type E. coli strain. Of note, however, the XL1-Blue E. coli K-12 strain exhibited a significant lag phase before multiplying and killing aphids. This bacterial strain has recently been shown to be more sensitive to oxidative stress than other E. coli K-12 strains, revealing a potential role for reactive oxygen species-mediated defenses in the otherwise reduced aphid immune system.

  8. Computational Assay of H7N9 Influenza Neuraminidase Reveals R292K Mutation Reduces Drug Binding Affinity

    NASA Astrophysics Data System (ADS)

    Woods, Christopher J.; Malaisree, Maturos; Long, Ben; McIntosh-Smith, Simon; Mulholland, Adrian J.

    2013-12-01

    The emergence of a novel H7N9 avian influenza that infects humans is a serious cause for concern. Of the genome sequences of H7N9 neuraminidase available, one contains a substitution of arginine to lysine at position 292, suggesting a potential for reduced drug binding efficacy. We have performed molecular dynamics simulations of oseltamivir, zanamivir and peramivir bound to H7N9, H7N9-R292K, and a structurally related H11N9 neuraminidase. They show that H7N9 neuraminidase is structurally homologous to H11N9, binding the drugs in identical modes. The simulations reveal that the R292K mutation disrupts drug binding in H7N9 in a comparable manner to that observed experimentally for H11N9-R292K. Absolute binding free energy calculations with the WaterSwap method confirm a reduction in binding affinity. This indicates that the efficacy of antiviral drugs against H7N9-R292K will be reduced. Simulations can assist in predicting disruption of binding caused by mutations in neuraminidase, thereby providing a computational `assay.'

  9. Microbial Community Succession during Lactate Amendment and Electron Acceptor Limitation Reveals a Predominance of Metal-Reducing Pelosinus spp.

    PubMed Central

    Mosher, Jennifer J.; Phelps, Tommy J.; Podar, Mircea; Hurt, Richard A.; Campbell, James H.; Drake, Meghan M.; Moberly, James G.; Schadt, Christopher W.; Brown, Steven D.; Hazen, Terry C.; Arkin, Adam P.; Palumbo, Anthony V.; Faybishenko, Boris A.

    2012-01-01

    The determination of the success of in situ bioremediation strategies is complex. By using controlled laboratory conditions, the influence of individual variables, such as U(VI), Cr(VI), and electron donors and acceptors on community structure, dynamics, and the metal-reducing potential can be studied. Triplicate anaerobic, continuous-flow reactors were inoculated with Cr(VI)-contaminated groundwater from the Hanford, WA, 100-H area, amended with lactate, and incubated for 95 days to obtain stable, enriched communities. The reactors were kept anaerobic with N2 gas (9 ml/min) flushing the headspace and were fed a defined medium amended with 30 mM lactate and 0.05 mM sulfate with a 48-h generation time. The resultant diversity decreased from 63 genera within 12 phyla to 11 bacterial genera (from 3 phyla) and 2 archaeal genera (from 1 phylum). Final communities were dominated by Pelosinus spp. and to a lesser degree, Acetobacterium spp., with low levels of other organisms, including methanogens. Four new strains of Pelosinus were isolated, with 3 strains being capable of Cr(VI) reduction while one also reduced U(VI). Under limited sulfate, it appeared that the sulfate reducers, including Desulfovibrio spp., were outcompeted. These results suggest that during times of electron acceptor limitation in situ, organisms such as Pelosinus spp. may outcompete the more-well-studied organisms while maintaining overall metal reduction rates and extents. Finally, lab-scale simulations can test new strategies on a smaller scale while facilitating community member isolation, so that a deeper understanding of community metabolism can be revealed. PMID:22267668

  10. Microbial community succession during lactate amendment and electron acceptor limitation reveals a predominance of metal-reducing Pelosinus spp.

    PubMed

    Mosher, Jennifer J; Phelps, Tommy J; Podar, Mircea; Hurt, Richard A; Campbell, James H; Drake, Meghan M; Moberly, James G; Schadt, Christopher W; Brown, Steven D; Hazen, Terry C; Arkin, Adam P; Palumbo, Anthony V; Faybishenko, Boris A; Elias, Dwayne A

    2012-04-01

    The determination of the success of in situ bioremediation strategies is complex. By using controlled laboratory conditions, the influence of individual variables, such as U(VI), Cr(VI), and electron donors and acceptors on community structure, dynamics, and the metal-reducing potential can be studied. Triplicate anaerobic, continuous-flow reactors were inoculated with Cr(VI)-contaminated groundwater from the Hanford, WA, 100-H area, amended with lactate, and incubated for 95 days to obtain stable, enriched communities. The reactors were kept anaerobic with N(2) gas (9 ml/min) flushing the headspace and were fed a defined medium amended with 30 mM lactate and 0.05 mM sulfate with a 48-h generation time. The resultant diversity decreased from 63 genera within 12 phyla to 11 bacterial genera (from 3 phyla) and 2 archaeal genera (from 1 phylum). Final communities were dominated by Pelosinus spp. and to a lesser degree, Acetobacterium spp., with low levels of other organisms, including methanogens. Four new strains of Pelosinus were isolated, with 3 strains being capable of Cr(VI) reduction while one also reduced U(VI). Under limited sulfate, it appeared that the sulfate reducers, including Desulfovibrio spp., were outcompeted. These results suggest that during times of electron acceptor limitation in situ, organisms such as Pelosinus spp. may outcompete the more-well-studied organisms while maintaining overall metal reduction rates and extents. Finally, lab-scale simulations can test new strategies on a smaller scale while facilitating community member isolation, so that a deeper understanding of community metabolism can be revealed.

  11. Persistent Homology in Sparse Regression and Its Application to Brain Morphometry

    PubMed Central

    Hanson, Jamie L.; Ye, Jieping; Davidson, Richard J.; Pollak, Seth D.

    2015-01-01

    Sparse systems are usually parameterized by a tuning parameter that determines the sparsity of the system. How to choose the right tuning parameter is a fundamental and difficult problem in learning the sparse system. In this paper, by treating the the tuning parameter as an additional dimension, persistent homological structures over the parameter space is introduced and explored. The structures are then further exploited in drastically speeding up the computation using the proposed soft-thresholding technique. The topological structures are further used as multivariate features in the tensor-based morphometry (TBM) in characterizing white matter alterations in children who have experienced severe early life stress and maltreatment. These analyses reveal that stress-exposed children exhibit more diffuse anatomical organization across the whole white matter region. PMID:25823032

  12. The Distribution of Thermophilic Sulfate-reducing Bacteria Along an Estuarine Gradient Reveals Multiple Origins of Endospores in Estuarine Sediments

    NASA Astrophysics Data System (ADS)

    Bell, E.

    2015-12-01

    Cold marine sediments harbour inactive spores of thermophilic bacteria. These misplaced thermophiles are genetically similar to microorganisms detected in deep biosphere environments, leading to the hypothesis that seabed fluid flow transports thermophiles out of warm subsurface environments and into the ocean. Estuaries form the transition between the marine and the terrestrial biosphere and are influenced by tidal currents, surface run-off and groundwater seepage. Endospores from thermophilic bacteria present in estuarine sediments could therefore originate from a number of sources that may influence the estuary differently. We have therefore tested the hypothesis that this will lead to a gradient in the composition of thermophilic endospore populations in estuarine sediments. The distribution of thermophilic spore-forming sulfate-reducing bacteria along an estuarine gradient from freshwater (River Tyne, UK) to marine (North Sea) was investigated. Microbial community analysis by 16S rRNA gene amplicon sequencing revealed changes in the thermophilic population enriched at different locations within the estuary. Certain species were only detected at the marine end, highlighting possible links to deep marine biosphere habitats such as oil reservoirs that harbour closely related Desulfotomaculum spp. Conversely, other taxa were predominantly observed in the freshwater reaches of the estuary indicating dispersal from an upstream or terrestrial source. Different endospore populations were enriched dependent on incubation temperature and spore heat-resistance. Microcosms incubated at 50, 60 or 70°C showed a shift in the dominant species of Desulfotomaculum enriched as the temperature increased. Microcosms triple-autoclaved at 121°C prior to incubation still showed rapid and reproducible sulfate-reduction and some Desulfotomaculum spp. remained active after autoclaving at 130°C. These results show that temperature physiology and biogeographic patterns can be used to

  13. Grey matter volume abnormalities in patients with bipolar I depressive disorder and unipolar depressive disorder: a voxel-based morphometry study.

    PubMed

    Cai, Yi; Liu, Jun; Zhang, Li; Liao, Mei; Zhang, Yan; Wang, Lifeng; Peng, Hongjun; He, Zhong; Li, Zexuan; Li, Weihui; Lu, Shaojia; Ding, Yuqiang; Li, Lingjiang

    2015-02-01

    Bipolar disorder and unipolar depressive disorder (UD) may be different in brain structure. In the present study, we performed voxel-based morphometry (VBM) to quantify the grey matter volumes in 23 patients with bipolar I depressive disorder (BP1) and 23 patients with UD, and 23 age-, gender-, and education-matched healthy controls (HCs) using magnetic resonance imaging. We found that compared with the HC and UD groups, the BP1 group showed reduced grey matter volumes in the right inferior frontal gyrus and middle cingulate gyrus, while the UD group showed reduced volume in the right inferior frontal gyrus compared to HCs. In addition, correlation analyses revealed that the grey matter volumes of these regions were negatively correlated with the Hamilton depression rating scores. Taken together, the results of our study suggest that decreased grey matter volume of the right inferior frontal gyrus is a common abnormality in BP1 and UD, and decreased grey matter volume in the right middle cingulate gyrus may be specific to BP1.

  14. APPLYING SPARSE CODING TO SURFACE MULTIVARIATE TENSOR-BASED MORPHOMETRY TO PREDICT FUTURE COGNITIVE DECLINE

    PubMed Central

    Zhang, Jie; Stonnington, Cynthia; Li, Qingyang; Shi, Jie; Bauer, Robert J.; Gutman, Boris A.; Chen, Kewei; Reiman, Eric M.; Thompson, Paul M.; Ye, Jieping; Wang, Yalin

    2016-01-01

    Alzheimer’s disease (AD) is a progressive brain disease. Accurate diagnosis of AD and its prodromal stage, mild cognitive impairment, is crucial for clinical trial design. There is also growing interests in identifying brain imaging biomarkers that help evaluate AD risk presymptomatically. Here, we applied a recently developed multivariate tensor-based morphometry (mTBM) method to extract features from hippocampal surfaces, derived from anatomical brain MRI. For such surface-based features, the feature dimension is usually much larger than the number of subjects. We used dictionary learning and sparse coding to effectively reduce the feature dimensions. With the new features, an Adaboost classifier was employed for binary group classification. In tests on publicly available data from the Alzheimers Disease Neuroimaging Initiative, the new framework outperformed several standard imaging measures in classifying different stages of AD. The new approach combines the efficiency of sparse coding with the sensitivity of surface mTBM, and boosts classification performance. PMID:27499829

  15. Unmasking of epigenetically silenced genes reveals DNA promoter methylation and reduced expression of PTCH in breast cancer.

    PubMed

    Wolf, Ido; Bose, Shikha; Desmond, Julian C; Lin, Bryan T; Williamson, Elizabeth A; Karlan, Beth Y; Koeffler, H Phillip

    2007-10-01

    A pharmacological-based global screen for epigenetically silenced tumor suppressor genes was performed in MCF-7 and MDA-MB-231 breast cancer cells. Eighty-one genes in MCF-7 cells and 131 in MDA-MB-231 cells were identified, that had low basal expression and were significantly upregulated following treatment. Eighteen genes were studied for methylation and/or expression in breast cancer; PTCH, the receptor for the hedgehog (Hh) pathway and a known tumor suppressor gene, was selected for further analysis. Methylation of the PTCH promoter was found in MCF-7 cells and in breast cancer samples, and correlated with low PTCH expression. Immunohistochemical analysis of breast tissue arrays revealed high expression of PTCH in normal breast compared to ductal carcinomas in situ (DCIS) and invasive ductal carcinomas; furthermore, association was found between PTCH expression and favorable prognostic factors. PTCH is an inhibitor of the Hh pathway, and its silencing activates the pathway and promotes growth. Indeed, high activity of the Hh pathway was identified in MCF-7 cells and overexpression of PTCH inhibited the pathway. Moreover, treatment with cyclopamine, an inhibitor of the pathway, reduced cell growth and slowed the cell cycle in these cells. Thus, unmasking of epigenetic silencing in breast cancer enabled us to discover a large number of candidate tumor suppressor genes. Further analysis suggested a role of one of these genes, PTCH, in breast cancer tumorigenesis.

  16. Calcaneal Tendon Collagen Fiber Morphometry and Aging.

    PubMed

    Hadraba, Daniel; Janacek, Jiri; Filova, Eva; Lopot, Frantisek; Paesen, Rik; Fanta, Ondrej; Jarman, Anneliese; Necas, Alois; Ameloot, Marcel; Jelen, Karel

    2017-10-01

    Fibrillar collagen in tendons and its natural development in rabbits are discussed in this paper. Achilles tendons from newborn (~7 days) to elderly (~38 months) rabbits were monitored in intact (n tendons=24) and microtome sectioned (n tendons=11) states with label-free second harmonic generation microscopy. After sectioning, the collagen fiber pattern was irregular for the younger animals and remained oriented parallel to the load axis of the tendon for the older animals. In contrast, the collagen fiber pattern in the intact samples followed the load axis for all the age groups. However, there was a significant difference in the tendon crimp pattern appearance between the age groups. The crimp amplitude (A) and wavelength (Λ) started at very low values (A=2.0±0.6 µm, Λ=19±4 µm) for the newborn animals. Both parameters increased for the sexually mature animals (>5 months old). When the animals were fully mature the amplitude decreased but the wavelength kept increasing. The results revealed that the microtome sectioning artifacts depend on the age of animals and that the collagen crimp pattern reflects the physical growth and development.

  17. Chromosome morphometry in opisthorchiid species (Platyhelminthes, Trematoda).

    PubMed

    Zadesenets, Kira S; Polyakov, Andrey V; Katokhin, Alexey V; Mordvinov, Viatcheslav A; Rubtsov, Nikolay B

    2017-08-01

    Few existing studies have dealt with cytogenetics in trematodes, largely due to the attendant technical difficulty of chromosome preparation. We performed a comparative analysis of chromosomes in five opistorchiid species, including Opisthorchis felineus Rivolta, 1884, Opisthorchis viverrini Poirier, 1886, Clonorchis sinensis Cobbold, 1875, Metorchis xanthosomus Creplin 1846, and Metorchis bilis (Braun, 1790) Odening, 1962. For some of these species, no detailed morphometric description of their karyotypes has yet been published; for the karyotype of Metorchis bilis this is the first-ever description. We found that opisthorchiids, like other trematodes, are characterized by karyotypic conservatism (N=6-7) and karyotype asymmetry, although comparison of chromosome morphometric traits did reveal differences between the karyotypes of the species. Moreover, to address certain a methodological issue in trematode chromosome preparation, we analyzed how the source of chromosomal material (partenitae or mature flukes) and the chromosome preparation techniques used (air-drying and cell suspension methods) affected chromosome spreading and size, concluding that the most reliable comparative method involves comparing relative parameters (relative length, arm ratio, centromeric index) of chromosomes prepared using the same technique. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  18. Robust tumor morphometry in multispectral fluorescence microscopy

    NASA Astrophysics Data System (ADS)

    Tabesh, Ali; Vengrenyuk, Yevgen; Teverovskiy, Mikhail; Khan, Faisal M.; Sapir, Marina; Powell, Douglas; Mesa-Tejada, Ricardo; Donovan, Michael J.; Fernandez, Gerardo

    2009-02-01

    Morphological and architectural characteristics of primary tissue compartments, such as epithelial nuclei (EN) and cytoplasm, provide important cues for cancer diagnosis, prognosis, and therapeutic response prediction. We propose two feature sets for the robust quantification of these characteristics in multiplex immunofluorescence (IF) microscopy images of prostate biopsy specimens. To enable feature extraction, EN and cytoplasm regions were first segmented from the IF images. Then, feature sets consisting of the characteristics of the minimum spanning tree (MST) connecting the EN and the fractal dimension (FD) of gland boundaries were obtained from the segmented compartments. We demonstrated the utility of the proposed features in prostate cancer recurrence prediction on a multi-institution cohort of 1027 patients. Univariate analysis revealed that both FD and one of the MST features were highly effective for predicting cancer recurrence (p <= 0.0001). In multivariate analysis, an MST feature was selected for a model incorporating clinical and image features. The model achieved a concordance index (CI) of 0.73 on the validation set, which was significantly higher than the CI of 0.69 for the standard multivariate model based solely on clinical features currently used in clinical practice (p < 0.0001). The contributions of this work are twofold. First, it is the first demonstration of the utility of the proposed features in morphometric analysis of IF images. Second, this is the largest scale study of the efficacy and robustness of the proposed features in prostate cancer prognosis.

  19. Monogenean anchor morphometry: systematic value, phylogenetic signal, and evolution

    PubMed Central

    Soo, Oi Yoon Michelle; Tan, Wooi Boon; Lim, Lee Hong Susan

    2016-01-01

    Background. Anchors are one of the important attachment appendages for monogenean parasites. Common descent and evolutionary processes have left their mark on anchor morphometry, in the form of patterns of shape and size variation useful for systematic and evolutionary studies. When combined with morphological and molecular data, analysis of anchor morphometry can potentially answer a wide range of biological questions. Materials and Methods. We used data from anchor morphometry, body size and morphology of 13 Ligophorus (Monogenea: Ancyrocephalidae) species infecting two marine mugilid (Teleostei: Mugilidae) fish hosts: Moolgarda buchanani (Bleeker) and Liza subviridis (Valenciennes) from Malaysia. Anchor shape and size data (n = 530) were generated using methods of geometric morphometrics. We used 28S rRNA, 18S rRNA, and ITS1 sequence data to infer a maximum likelihood phylogeny. We discriminated species using principal component and cluster analysis of shape data. Adams’s Kmult was used to detect phylogenetic signal in anchor shape. Phylogeny-correlated size and shape changes were investigated using continuous character mapping and directional statistics, respectively. We assessed morphological constraints in anchor morphometry using phylogenetic regression of anchor shape against body size and anchor size. Anchor morphological integration was studied using partial least squares method. The association between copulatory organ morphology and anchor shape and size in phylomorphospace was used to test the Rohde-Hobbs hypothesis. We created monogeneaGM, a new R package that integrates analyses of monogenean anchor geometric morphometric data with morphological and phylogenetic data. Results. We discriminated 12 of the 13 Ligophorus species using anchor shape data. Significant phylogenetic signal was detected in anchor shape. Thus, we discovered new morphological characters based on anchor shaft shape, the length between the inner root point and the outer root

  20. Morphometry and Morphology of Fresh Craters on Titan

    NASA Astrophysics Data System (ADS)

    Kirk, R. L.; Wood, C. A.; Neish, C.; Lucas, A.; Hayes, A. G.; Cassini Radar Team

    2011-12-01

    Cassini RADAR imagery obtained on Titan flyby T77 revealed a 40-km diameter fresh impact crater at 11.6° N 44.6° W. This is only the 8th crater identified with high confidence (Wood et al., 2010, Icarus 206, 334), and the 3rd (after Sinlap D=79 km and Ksa D=30 km) for which the depth can be estimated by comparing the foreshortening of the near and far walls. This "autostereo" technique yields an estimated depth of 680 m. The T77 image forms a stereo pair with the T17 discovery image of Ksa from which we estimate the depth of Ksa at 750-800 m, in close agreement with SARTopo data. The depth of Sinlap is 760 m based on SARTopo. Depth-diameter ratios for these craters thus range from 0.01 to 0.025 and the depths are comparable to but 200-400 m shallower than fresh craters of the same size on Ganymede (Bray et al., 2008, Met. Planet Sci. 43, 1979). The depth differences could be explained by initial crater morphometry, by relaxation in a different thermal environment, or (perhaps most plausibly given the bland floors of even the freshest Titan craters) to sedimentary infill. In contrast, the 18x36 km elliptical depression at Sotra Facula is much deeper than Ganymede craters of similar size (d=1500 m from stereo), supporting the conclusion that it is not an impact crater. All three craters exhibit a relatively radar-bright annulus around the outer edge of the floor, possibly as the result of mass wasting of blocky materials from the crater walls. The central part of each crater is darker. The central darker floor of the new crater is symmetrical and featureless, whereas Ksa has a bright central ring 7 km in diameter. Stereo spot heights indicate the ring is 350±100 m above the outer floor. This height is in close agreement with the scaling for Ganymede crater central peaks from Bray et al. (2008). The darker floor area of Sinlap is substantially asymmetrical with a small bright central spot whose elevation is unknown. The new crater has continuous, radar

  1. Experimentally reduced root–microbe interactions reveal limited plasticity in functional root traits in Acer and Quercus

    PubMed Central

    Lee, Mei-Ho; Comas, Louise H.; Callahan, Hilary S.

    2014-01-01

    Background and Aims Interactions between roots and soil microbes are critical components of below-ground ecology. It is essential to quantify the magnitude of root trait variation both among and within species, including variation due to plasticity. In addition to contextualizing the magnitude of plasticity relative to differences between species, studies of plasticity can ascertain if plasticity is predictable and whether an environmental factor elicits changes in traits that are functionally advantageous. Methods To compare functional traits and trait plasticities in fine root tissues with natural and reduced levels of colonization by microbial symbionts, trimmed and surface-sterilized root segments of 2-year-old Acer rubrum and Quercus rubra seedlings were manipulated. Segments were then replanted into satellite pots filled with control or heat-treated soil, both originally derived from a natural forest. Mycorrhizal colonization was near zero in roots grown in heat-treated soil; roots grown in control soil matched the higher colonization levels observed in unmanipulated root samples collected from field locations. Key Results Between-treatment comparisons revealed negligible plasticity for root diameter, branching intensity and nitrogen concentration across both species. Roots from treated soils had decreased tissue density (approx. 10–20 %) and increased specific root length (approx. 10–30 %). In contrast, species differences were significant and greater than treatment effects in traits other than tissue density. Interspecific trait differences were also significant in field samples, which generally resembled greenhouse samples. Conclusions The combination of experimental and field approaches was useful for contextualizing trait plasticity in comparison with inter- and intra-specific trait variation. Findings that root traits are largely species dependent, with the exception of root tissue density, are discussed in the context of current literature on root

  2. Genotyping of whole genome amplified reduced representation libraries reveals a cryptic population of Culicoides brevitarsis in the Northern Territory, Australia.

    PubMed

    Onyango, Maria G; Aitken, Nicola C; Jack, Cameron; Chuah, Aaron; Oguya, James; Djikeng, Appolinaire; Kemp, Steve; Bellis, Glenn A; Nicholas, Adrian; Walker, Peter J; Duchemin, Jean-Bernard

    2016-09-30

    The advent of genotyping by Next Generation Sequencing has enabled rapid discovery of thousands of single nucleotide polymorphism (SNP) markers and high throughput genotyping of large populations at an affordable cost. Genotyping by sequencing (GBS), a reduced representation library sequencing method, allows highly multiplexed sequencing of genomic subsets. This method has limitations for small organisms with low amounts of genomic DNA, such as the bluetongue virus (BTV) vectors, Culicoides midges. This study employed the GBS method to isolate SNP markers de novo from whole genome amplified Culicoides brevitarsis genomic DNA. The individuals were collected from regions representing two different Australian patterns of BTV strain distribution: the Northern Territory (NT) and the east coast. We isolated 8145 SNPs using GBS. Phylogenetic analysis conducted using the filtered 3263 SNPs revealed the presence of a distinct C. brevitarsis sub-population in the NT and this was confirmed by analysis of mitochondrial DNA. Two loci showed a very strong signal for selection and were unique to the NT population. Bayesian analysis with STRUCTURE indicated a possible two-population cluster. The results suggest that genotyping vectors with high density markers in combination with biological and environmental data is useful. However, more extensive sampling over a wider spatial and temporal range is needed. The presence of sub-structure in populations and loci under natural selection indicates the need for further investigation of the role of vectors in shaping the two Australian systems of BTV transmission. The described workflow is transferable to genotyping of small, non-model organisms, including arthropod vectors of pathogens of economic and medical importance.

  3. Experimentally reduced root-microbe interactions reveal limited plasticity in functional root traits in Acer and Quercus.

    PubMed

    Lee, Mei-Ho; Comas, Louise H; Callahan, Hilary S

    2014-02-01

    Interactions between roots and soil microbes are critical components of below-ground ecology. It is essential to quantify the magnitude of root trait variation both among and within species, including variation due to plasticity. In addition to contextualizing the magnitude of plasticity relative to differences between species, studies of plasticity can ascertain if plasticity is predictable and whether an environmental factor elicits changes in traits that are functionally advantageous. To compare functional traits and trait plasticities in fine root tissues with natural and reduced levels of colonization by microbial symbionts, trimmed and surface-sterilized root segments of 2-year-old Acer rubrum and Quercus rubra seedlings were manipulated. Segments were then replanted into satellite pots filled with control or heat-treated soil, both originally derived from a natural forest. Mycorrhizal colonization was near zero in roots grown in heat-treated soil; roots grown in control soil matched the higher colonization levels observed in unmanipulated root samples collected from field locations. Between-treatment comparisons revealed negligible plasticity for root diameter, branching intensity and nitrogen concentration across both species. Roots from treated soils had decreased tissue density (approx. 10-20 %) and increased specific root length (approx. 10-30 %). In contrast, species differences were significant and greater than treatment effects in traits other than tissue density. Interspecific trait differences were also significant in field samples, which generally resembled greenhouse samples. The combination of experimental and field approaches was useful for contextualizing trait plasticity in comparison with inter- and intra-specific trait variation. Findings that root traits are largely species dependent, with the exception of root tissue density, are discussed in the context of current literature on root trait variation, interactions with symbionts and recent

  4. Computer automated sperm head morphometry analysis (ASMA) of goat spermatozoa.

    PubMed

    Gravance, C G; Lewis, K M; Casey, P J

    1995-11-01

    The development of computer automated sperm morphometry analysis (ASMA) allows for the objective analysis of sperm head dimensions. A number of studies have been performed to optimize the efficiency of these systems when analyzing spermatozoa from a variety of species. In this study, frozen semen from 10 fertile goat bucks was thawed and prepared on slides for morphometric analysis to evaluate technical variation and to standardize ASMA procedures for goat spermatozoa. Methods of staining, the number of spermatozoa necessary to sample and optimal microscopic magnification were assessed. Staining for 20 min in hematoxylin (HEM) was found to be optimal. The most efficient method of analyzing goat sperm morphometry was to evaluate 100 sperm cells at x20 objective magnification. Using these techniques, a sample could be analyzed in approximately 2 min. The system properly recognized and digitized spermatozoa 96% of the time with a target recognition error rate of less than 1%. The morphometric measurements of sperm heads for all 10 bucks were the following: length = 7.69microm, width = 3.80microm, width/length ratio = 0.5, area = 22.82microm and perimeter = 20.15microm. The mean coefficients of variation (CV) for all bucks ranged from 3.4% for length to 5.8% for area. Standardized sample preparation techniques and analysis were found to improve the efficiency of ASMA.

  5. Pelvic Belt Effects on Pelvic Morphometry, Muscle Activity and Body Balance in Patients with Sacroiliac Joint Dysfunction

    PubMed Central

    Soisson, Odette; Lube, Juliane; Germano, Andresa; Hammer, Karl-Heinz; Josten, Christoph; Sichting, Freddy; Winkler, Dirk; Milani, Thomas L.; Hammer, Niels

    2015-01-01

    Introduction The sacroiliac joint (SIJ) is frequently involved in low back and pelvic girdle pain. However, morphometrical and functional characteristics related to SIJ pain are poorly defined. Pelvic belts represent one treatment option, but evidence still lacks as to their pain-reducing effects and the mechanisms involved. Addressing these two issues, this case-controlled study compares morphometric, functional and clinical data in SIJ patients and healthy controls and evaluates the effects of short-term pelvic belt application. Methods Morphometric and functional data pertaining to pelvic belt effects were compared in 17 SIJ patients and 17 controls. Lumbar spine and pelvis morphometries were obtained from 3T magnetic resonance imaging. Functional electromyography data of pelvis and leg muscles and center of pressure excursions were measured in one-leg stance. The numerical rating scale was used to evaluate immediate pain-reducing effects. Results Pelvic morphometry was largely unaltered in SIJ patients and also by pelvic belt application. The angle of lumbar lateral flexion was significantly larger in SIJ patients without belt application. Muscle activity and center of pressure were unaffected by SIJ pain or by belt application in one-leg stance. Nine of 17 patients reported decreased pain intensities under moderate belt application, four reported no change and four reported increased pain intensity. For the entire population investigated here, this qualitative description was not confirmed on a statistical significant level. Discussion Minute changes were observed in the alignment of the lumbar spine in the frontal plane in SIJ patients. The potential pain-decreasing effects of pelvic belts could not be attributed to altered muscle activity, pelvic morphometry or body balance in a static short-term application. Long-term belt effects will therefore be of prospective interest. PMID:25781325

  6. Gray Matter Alterations in Adults with Attention-Deficit/Hyperactivity Disorder Identified by Voxel Based Morphometry

    PubMed Central

    Seidman, Larry J.; Biederman, Joseph; Liang, Lichen; Valera, Eve M.; Monuteaux, Michael C.; Brown, Ariel; Kaiser, Jonathan; Spencer, Thomas; Faraone, Stephen V.; Makris, Nikos

    2014-01-01

    Background Gray and white matter volume deficits have been reported in many structural magnetic resonance imaging (MRI) studies of children with attention-deficit/hyperactivity disorder (ADHD); however, there is a paucity of structural MRI studies of adults with ADHD. This study used voxel based morphometry and applied an a priori region of interest approach based on our previous work, as well as from well-developed neuroanatomical theories of ADHD. Methods Seventy-four adults with DSM-IV ADHD and 54 healthy control subjects comparable on age, sex, race, handedness, IQ, reading achievement, frequency of learning disabilities, and whole brain volume had an MRI on a 1.5T Siemens scanner. A priori region of interest hypotheses focused on reduced volumes in ADHD in dorsolateral prefrontal cortex, anterior cingulate cortex, caudate, putamen, inferior parietal lobule, and cerebellum. Analyses were carried out by FSL-VBM 1.1. Results Relative to control subjects, ADHD adults had significantly smaller gray matter volumes in parts of six of these regions at p ≤ .01, whereas parts of the dorsolateral prefrontal cortex and inferior parietal lobule were significantly larger in ADHD at this threshold. However, a number of other regions were smaller and larger in ADHD (especially fronto-orbital cortex) at this threshold. Only the caudate remained significantly smaller at the family-wise error rate. Conclusions Adults with ADHD have subtle volume reductions in the caudate and possibly other brain regions involved in attention and executive control supporting frontostriatal models of ADHD. Modest group brain volume differences are discussed in the context of the nature of the samples studied and voxel based morphometry methodology. PMID:21183160

  7. Gray matter alterations in adults with attention-deficit/hyperactivity disorder identified by voxel based morphometry.

    PubMed

    Seidman, Larry J; Biederman, Joseph; Liang, Lichen; Valera, Eve M; Monuteaux, Michael C; Brown, Ariel; Kaiser, Jonathan; Spencer, Thomas; Faraone, Stephen V; Makris, Nikos

    2011-05-01

    Gray and white matter volume deficits have been reported in many structural magnetic resonance imaging (MRI) studies of children with attention-deficit/hyperactivity disorder (ADHD); however, there is a paucity of structural MRI studies of adults with ADHD. This study used voxel based morphometry and applied an a priori region of interest approach based on our previous work, as well as from well-developed neuroanatomical theories of ADHD. Seventy-four adults with DSM-IV ADHD and 54 healthy control subjects comparable on age, sex, race, handedness, IQ, reading achievement, frequency of learning disabilities, and whole brain volume had an MRI on a 1.5T Siemens scanner. A priori region of interest hypotheses focused on reduced volumes in ADHD in dorsolateral prefrontal cortex, anterior cingulate cortex, caudate, putamen, inferior parietal lobule, and cerebellum. Analyses were carried out by FSL-VBM 1.1. Relative to control subjects, ADHD adults had significantly smaller gray matter volumes in parts of six of these regions at p ≤ .01, whereas parts of the dorsolateral prefrontal cortex and inferior parietal lobule were significantly larger in ADHD at this threshold. However, a number of other regions were smaller and larger in ADHD (especially fronto-orbital cortex) at this threshold. Only the caudate remained significantly smaller at the family-wise error rate. Adults with ADHD have subtle volume reductions in the caudate and possibly other brain regions involved in attention and executive control supporting frontostriatal models of ADHD. Modest group brain volume differences are discussed in the context of the nature of the samples studied and voxel based morphometry methodology. Copyright © 2011 Society of Biological Psychiatry. Published by Elsevier Inc. All rights reserved.

  8. Brainstem dysfunction in patients with late-onset Lennox-Gastaut syndrome: Voxel-based morphometry and tract-based spatial statistics study.

    PubMed

    Park, Kang Min; Hur, Yun Jung; Kim, Sung Eun

    2016-01-01

    There have been a few reports of patients who developed Lennox-Gastaut syndrome (LGS) in the second decades of their life. The aim of this study was to investigate electroclinical presentation in patients with late-onset LGS. In addition, we evaluated structural abnormalities of the brain, which may give some clue about the common pathogenic pathway in LGS. We enrolled the patients with late-onset LGS. We collected electroclinical characteristics of the patients and evaluated structural abnormalities using voxel-based morphometry (VBM) and tract-based spatial statistics (TBSS) analysis. The three subjects were diagnosed with late-onset LGS. The patients have no mental retardation and normal background activities on electroencephalography (EEG), and they had generalized paroxysmal fast activities on EEG, especially during sleep. The TBSS analysis revealed that fractional anisotropy values in the patients were significantly reduced in the white matter of brainstem compared with normal controls. However, VBM analysis did not show any significant difference between the patients and normal controls. Patients with late-onset LGS have different clinical and EEG characteristics from those with early-onset LGS. In addition, we demonstrated that brainstem dysfunction might contribute to the pathogenesis of late-onset LGS.

  9. A voxel-based morphometry study of grey matter loss in fragile X-associated tremor/ataxia syndrome.

    PubMed

    Hashimoto, Ryu-ichiro; Javan, Alireza K; Tassone, Flora; Hagerman, Randi J; Rivera, Susan M

    2011-03-01

    Fragile X-associated tremor/ataxia syndrome is a neurodegenerative disorder that primarily affects older male premutation carriers of the fragile X mental retardation gene. Although its core symptoms are mainly characterized by motor problems such as intention tremor and gait ataxia, cognitive decline and psychiatric problems are also commonly observed. Past radiological and histological approaches have focused on prominent neurodegenerative changes in specific brain structures including the cerebellum and limbic areas. However, quantitative investigations of the regional structural abnormalities have not been performed over the whole brain. In this study, we adopted the voxel-based morphometry method together with regions of interest analysis for the cerebellum to examine the pattern of regional grey matter change in the male premutation carriers with and without fragile X-associated tremor/ataxia syndrome. In a comparison with healthy controls, we found striking grey matter loss of the patients with fragile X-associated tremor/ataxia syndrome in multiple regions over the cortical and subcortical structures. In the cerebellum, the anterior lobe and the superior posterior lobe were profoundly reduced in both vermis and hemispheres. In the cerebral cortex, clusters of highly significant grey matter reduction were found in the extended areas in the medial surface of the brain, including the dorsomedial prefrontal cortex, anterior cingulate cortex and precuneus. The other prominent grey matter loss was found in the lateral prefrontal cortex, orbitofrontal cortex, amygdala and insula. Although the voxel-wise comparison between the asymptomatic premutation group and healthy controls did not reach significant difference, a regions of interest analysis revealed significant grey matter reduction in anterior subregions of the cerebellar vermis and hemisphere in the asymptomatic premutation group. Correlation analyses using behavioural scales of the premutation groups showed

  10. Creativity and borderline personality disorder: evidence from a voxel-based morphometry study.

    PubMed

    Leutgeb, Verena; Ille, Rottraut; Wabnegger, Albert; Schienle, Anne; Schöggl, Helmut; Weber, Bernhard; Papousek, Ilona; Weiss, Elisabeth M; Fink, Andreas

    2016-05-01

    Throughout the history, various examples of eminent creative people suffering from mental disorders along with some empirical research reports strengthened the idea of a potential link between creativity and psychopathology. This study investigated different facets of psychometrically determined creativity in 20 females diagnosed with borderline personality disorder (BPD) relative to 19 healthy female controls. In addition, group differences in grey matter (GM) were examined. Behavioural findings revealed no significant differences between the BPD group and healthy controls with respect to verbal and figural-graphic creative task performance and creativity-related personality characteristics. Whole-brain voxel-based morphometry analyses revealed a distinct pattern of GM reductions in the BPD group (relative to controls) in a network of brain regions closely associated with various cognitive and emotional functions (including the bilateral orbital inferior frontal gyri and the left superior temporal gyrus), partly overlapping with creativity-related brain regions. Correlation analyses moreover revealed that in the BPD group GM reductions in the orbital parts of the inferior and middle frontal gyri were associated with lower levels of creativity. This study provides no indications in favour of the putative link between creativity and psychopathology, as sometimes reported in the literature.

  11. Morphometry and land cover based multi-criteria analysis for assessing the soil erosion susceptibility of the western Himalayan watershed.

    PubMed

    Altaf, Sadaff; Meraj, Gowhar; Romshoo, Shakil Ahmad

    2014-12-01

    Complex mountainous environments such as Himalayas are highly susceptibility to natural hazards particular those that are triggered by the action of water such as floods, soil erosion, mass movements and siltation of the hydro-electric power dams. Among all the natural hazards, soil erosion is the most implicit and the devastating hazard affecting the life and property of the millions of people living in these regions. Hence to review and devise strategies to reduce the adverse impacts of soil erosion is of utmost importance to the planners of watershed management programs in these regions. This paper demonstrates the use of satellite based remote sensing data coupled with the observational field data in a multi-criteria analytical (MCA) framework to estimate the soil erosion susceptibility of the sub-watersheds of the Rembiara basin falling in the western Himalaya, using geographical information system (GIS). In this paper, watershed morphometry and land cover are used as an inputs to the MCA framework to prioritize the sub-watersheds of this basin on the basis of their different susceptibilities to soil erosion. Methodology included the derivation of a set of drainage and land cover parameters that act as the indicators of erosion susceptibility. Further the output from the MCA resulted in the categorization of the sub-watersheds into low, medium, high and very high erosion susceptibility classes. A detailed prioritization map for the susceptible sub-watersheds based on the combined role of land cover and morphometry is finally presented. Besides, maps identifying the susceptible sub-watersheds based on morphometry and land cover only are also presented. The results of this study are part of the watershed management program in the study area and are directed to instigate appropriate measures to alleviate the soil erosion in the study area.

  12. Significant Association between Sulfate-Reducing Bacteria and Uranium-Reducing Microbial Communities as Revealed by a Combined Massively Parallel Sequencing-Indicator Species Approach▿ †

    PubMed Central

    Cardenas, Erick; Wu, Wei-Min; Leigh, Mary Beth; Carley, Jack; Carroll, Sue; Gentry, Terry; Luo, Jian; Watson, David; Gu, Baohua; Ginder-Vogel, Matthew; Kitanidis, Peter K.; Jardine, Philip M.; Zhou, Jizhong; Criddle, Craig S.; Marsh, Terence L.; Tiedje, James M.

    2010-01-01

    Massively parallel sequencing has provided a more affordable and high-throughput method to study microbial communities, although it has mostly been used in an exploratory fashion. We combined pyrosequencing with a strict indicator species statistical analysis to test if bacteria specifically responded to ethanol injection that successfully promoted dissimilatory uranium(VI) reduction in the subsurface of a uranium contamination plume at the Oak Ridge Field Research Center in Tennessee. Remediation was achieved with a hydraulic flow control consisting of an inner loop, where ethanol was injected, and an outer loop for flow-field protection. This strategy reduced uranium concentrations in groundwater to levels below 0.126 μM and created geochemical gradients in electron donors from the inner-loop injection well toward the outer loop and downgradient flow path. Our analysis with 15 sediment samples from the entire test area found significant indicator species that showed a high degree of adaptation to the three different hydrochemical-created conditions. Castellaniella and Rhodanobacter characterized areas with low pH, heavy metals, and low bioactivity, while sulfate-, Fe(III)-, and U(VI)-reducing bacteria (Desulfovibrio, Anaeromyxobacter, and Desulfosporosinus) were indicators of areas where U(VI) reduction occurred. The abundance of these bacteria, as well as the Fe(III) and U(VI) reducer Geobacter, correlated with the hydraulic connectivity to the substrate injection site, suggesting that the selected populations were a direct response to electron donor addition by the groundwater flow path. A false-discovery-rate approach was implemented to discard false-positive results by chance, given the large amount of data compared. PMID:20729318

  13. Metabolomics reveals the mechanisms for the cardiotoxicity of Pinelliae Rhizoma and the toxicity-reducing effect of processing

    PubMed Central

    Su, Tao; Tan, Yong; Tsui, Man-Shan; Yi, Hua; Fu, Xiu-Qiong; Li, Ting; Chan, Chi Leung; Guo, Hui; Li, Ya-Xi; Zhu, Pei-Li; Tse, Anfernee Kai Wing; Cao, Hui; Lu, Ai-Ping; Yu, Zhi-Ling

    2016-01-01

    Pinelliae Rhizoma (PR) is a commonly used Chinese medicinal herb, but it has been frequently reported about its toxicity. According to the traditional Chinese medicine theory, processing can reduce the toxicity of the herbs. Here, we aim to determine if processing reduces the toxicity of raw PR, and to explore the underlying mechanisms of raw PR-induced toxicities and the toxicity-reducing effect of processing. Biochemical and histopathological approaches were used to evaluate the toxicities of raw and processed PR. Rat serum metabolites were analyzed by LC-TOF-MS. Ingenuity pathway analysis of the metabolomics data highlighted the biological pathways and network functions involved in raw PR-induced toxicities and the toxicity-reducing effect of processing, which were verified by molecular approaches. Results showed that raw PR caused cardiotoxicity, and processing reduced the toxicity. Inhibition of mTOR signaling and activation of the TGF-β pathway contributed to raw PR-induced cardiotoxicity, and free radical scavenging might be responsible for the toxicity-reducing effect of processing. Our data shed new light on the mechanisms of raw PR-induced cardiotoxicity and the toxicity-reducing effect of processing. This study provides scientific justifications for the traditional processing theory of PR, and should help in optimizing the processing protocol and clinical combinational application of PR. PMID:27698376

  14. Metabolomics reveals the mechanisms for the cardiotoxicity of Pinelliae Rhizoma and the toxicity-reducing effect of processing

    NASA Astrophysics Data System (ADS)

    Su, Tao; Tan, Yong; Tsui, Man-Shan; Yi, Hua; Fu, Xiu-Qiong; Li, Ting; Chan, Chi Leung; Guo, Hui; Li, Ya-Xi; Zhu, Pei-Li; Tse, Anfernee Kai Wing; Cao, Hui; Lu, Ai-Ping; Yu, Zhi-Ling

    2016-10-01

    Pinelliae Rhizoma (PR) is a commonly used Chinese medicinal herb, but it has been frequently reported about its toxicity. According to the traditional Chinese medicine theory, processing can reduce the toxicity of the herbs. Here, we aim to determine if processing reduces the toxicity of raw PR, and to explore the underlying mechanisms of raw PR-induced toxicities and the toxicity-reducing effect of processing. Biochemical and histopathological approaches were used to evaluate the toxicities of raw and processed PR. Rat serum metabolites were analyzed by LC-TOF-MS. Ingenuity pathway analysis of the metabolomics data highlighted the biological pathways and network functions involved in raw PR-induced toxicities and the toxicity-reducing effect of processing, which were verified by molecular approaches. Results showed that raw PR caused cardiotoxicity, and processing reduced the toxicity. Inhibition of mTOR signaling and activation of the TGF-β pathway contributed to raw PR-induced cardiotoxicity, and free radical scavenging might be responsible for the toxicity-reducing effect of processing. Our data shed new light on the mechanisms of raw PR-induced cardiotoxicity and the toxicity-reducing effect of processing. This study provides scientific justifications for the traditional processing theory of PR, and should help in optimizing the processing protocol and clinical combinational application of PR.

  15. Investigations of Martian Impact Crater Morphologies and Morphometries

    NASA Technical Reports Server (NTRS)

    Barlow, Nadine G.

    2002-01-01

    We have made substantial progress towards completion of the original objectives and are continuing to include new data from the Mars Global Surveyor MOC and TES instruments as they become available (the MOLA instrument has ceased operation as of 2002). The project funding has been used to provide salary support to the PI and several undergraduate students, cover publication charges for two papers, reimburse travel expenses to conferences and workshops incurred by the PI and students, and cover a number of other expenses such as software upgrades and production costs of slides and color prints. This study is revising the PI's Catalog of Large Martian Impact Craters with information obtained from MGS and is utilizing data in the revised Catalog to investigate which planetary factors (such as location, elevation, terrain type, etc.) primarily affect the formation of specific ejecta morphologies and morphometries.

  16. Martian Fretted Terrain Morphometry Interpreted Using Principal Components Analysis

    NASA Technical Reports Server (NTRS)

    Kochell, R. C.

    1985-01-01

    Martian fretted terrain is an extensive area of complex topography characterized by smooth, flat-floor valleys and mesas separated by abrupt escarpments along the boundary of heavily cratered uplands. The Deuteronilus-Protonilus region of the fretted terrain between latitude 35 degrees N and 50 degrees N and between 305 degrees W and 350 degrees W longitude was selected for quantitative landform study with the use of principal components analysis (PCA). The morphometry of upland mesa remnants and debris aprons was digitized with respect to latitude, longitude, and distance from the cratered terrain boundary (CTB). The PCA demonstrates that there are definable spatial variations in morphology with respect to longitude and latitude which suggest that the degradation along the CTB proceeded toward the southwest. The PCA also showed that there are organized relationships within the fretted landforms irrespective of their location. Finally, PCA indicated that an orientation of the degraded mesas exists which may be controlled by structure.

  17. New experimental results in atlas-based brain morphometry

    NASA Astrophysics Data System (ADS)

    Gee, James C.; Fabella, Brian A.; Fernandes, Siddharth E.; Turetsky, Bruce I.; Gur, Ruben C.; Gur, Raquel E.

    1999-05-01

    In a previous meeting, we described a computational approach to MRI morphometry, in which a spatial warp mapping a reference or atlas image into anatomic alignment with the subject is first inferred. Shape differences with respect to the atlas are then studied by calculating the pointwise Jacobian determinant for the warp, which provides a measure of the change in differential volume about a point in the reference as it transforms to its corresponding position in the subject. In this paper, the method is used to analyze sex differences in the shape and size of the corpus callosum in an ongoing study of a large population of normal controls. The preliminary results of the current analysis support findings in the literature that have observed the splenium to be larger in females than in males.

  18. [Morphometry of the kidney. Applied study in urology and imaging].

    PubMed

    Sampaio, F J; Mandarim-de-Lacerda, C A

    1989-01-01

    A morphometric study was made on 100 human kidneys obtained by necropsies from 50 cadavers without renal pathology and ranging in age from 16 of 60 years (32.0 +/- 12.1 years). The results of the renal measures showed the following averages: length (right kidney 10.97 cm; left kidney = 11.21.cm), Width of the superior pole (right kidney = 6.40 cm; left kidney = 6.48 cm), width of the inferior pole (right kidney = 5.59 cm; left kidney = 5.39 cm), thickness (right kidney = 3.21 cm; left kidney = 3.37 cm). Left kidney presented usually greater length, greater width and greater thickness than right kidney. There are positive relations between several measures of the renal morphometry. Allometric method was used in order to study the correlation renal length vs body length and to make the curves.

  19. Gill morphometry of the red drum, Sciaenops ocellatus.

    PubMed

    Don Stevens, E

    1992-08-01

    The structure and morphometry of the gills of the marine teleost, red drum, have been studied. The present analysis of gas exchange area of fish gills is one of the most intensive and the results are compared to less intense averaging methods. Based on the gill area estimates, red drum falls into the category of a fish of intermediate activity. Its gill clearly has an exchange area less than that of the tunas, but is slightly greater than that of trout or bass. The three components that contribute to total exchange area (filament length, lamellar density, and area of individual lamellae) are not all greater in species with a greater total exchange area. The best correlate is total filament length.

  20. Adolescent drinking and brain morphometry: A co-twin control analysis.

    PubMed

    Wilson, Sylia; Malone, Stephen M; Thomas, Kathleen M; Iacono, William G

    2015-12-01

    Developmental changes in structure and functioning are thought to make the adolescent brain particularly sensitive to the negative effects of alcohol. Although alcohol use disorders are relatively rare in adolescence, the initiation of alcohol use, including problematic use, becomes increasingly prevalent during this period. The present study examined associations between normative drinking (alcohol initiation, binge drinking, intoxication) and brain morphometry in a sample of 96 adolescent monozygotic twins. A priori regions of interest included 11 subcortical and 20 cortical structures implicated in the existing empirical literature as associated with normative alcohol use in adolescence. In addition, co-twin control analyses were used to disentangle risk for alcohol use from consequences of alcohol exposure on the developing brain. Results indicated significant associations reflecting preexisting vulnerability toward problematic alcohol use, including reduced volume of the amygdala, increased volume of the cerebellum, and reduced cortical volume and thickness in several frontal and temporal regions, including the superior and middle frontal gyri, pars triangularis, and middle and inferior temporal gyri. Results also indicated some associations consistent with a neurotoxic effect of alcohol exposure, including reduced volume of the ventral diencephalon and the middle temporal gyrus. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

  1. Core/shell-type nanorods of Tb3+-doped LaPO4, modified with amine groups, revealing reduced cytotoxicity

    NASA Astrophysics Data System (ADS)

    Runowski, Marcin; Dąbrowska, Krystyna; Grzyb, Tomasz; Miernikiewicz, Paulina; Lis, Stefan

    2013-11-01

    A simple co-precipitation reaction between Ln3+ cations (Ln = lanthanide) and phosphate ions in the presence of polyethylene glycol (PEG), including post-treatment under hydrothermal conditions, leads to the formation of Tb3+-doped LaPO4 crystalline nanorods. The nanoparticles obtained can be successfully coated with amorphous and porous silica, forming core/shell-type nanorods. Both products reveal intensive green luminescence under UV lamp irradiation. The surface of the core/shell-type product can also be modified with -NH2 groups via silylation procedure, using 3-aminopropyltriethoxysilane as a modifier. Powder X-ray diffraction, transmission electron microscopy, and scanning electron microscopy confirm the desired structure and needle-like shape of the products synthesized. Fourier transform infrared spectroscopy and specific surface area measurements by Brunauer-Emmett-Teller method reveal a successful surface modification with amine groups of the core/shell-type nanoparticles prepared. The nanomaterials synthesized exhibit green luminescence characteristic of Tb3+ ions, as solid powders and aqueous colloids, examined by spectrofluorometry. The in vitro cytotoxicity studies reveal different degree toxicity of the products. LaPO4:Tb3+@SiO2@NH2 exhibits the smallest toxicity against B16F0 mouse melanoma cancer cells and human skin microvascular endothelial cell lines, in contrast to the most toxic LaPO4:Tb3+@SiO2.

  2. Identification of prevalent vertebral fractures using CT lateral scout views: a comparison of semi-automated quantitative vertebral morphometry and radiologist semi-quantitative grading

    PubMed Central

    Kim, Y. M.; Demissie, S.; Genant, H. K.; Cheng, X.; Yu, W.; Samelson, E. J.; Kiel, D. P.

    2013-01-01

    Summary We compared vertebral fracture assessment by semi-automated quantitative vertebral morphometry measurements with the conventional semi-quantitative (SQ) grading using lateral CT scout views. The semi-automated morphometry method showed good to excellent agreement with the visual SQ grading by radiologists for identification of vertebral fractures. Introduction Semi-automated quantitative vertebral morphometry (QM) measurements may enhance management of osteoporosis patients by providing an efficient means to identify vertebral fractures (VFx). We compared identification of prevalent VFx by semi-automated QM to SQ grading. Methods A non-radiologist performed semi-automated QM from CT lateral scout views in 200 subjects (102 men, 98 women, 65.8±8.9 years) selected from the Framingham Heart Study Multidetector CT Study. VFx were classified in the QM approach based on using Genant’s criteria for deformities, and compared with conventional SQ grading performed by experienced radiologists as the gold standard. The kappa (k) statistics, percent agreement (% Agree), sensitivity (SE), specificity (SP), positive predictive value (PPV), and negative predictive value (NPV) were computed. Results Among 200 subjects, 57 had mild and 41 had moderate or severe VFx by visual SQ grading. Per-person analyses showed excellent agreement between the two methods, with k=0.780. The % Agree ranged from 86.7% to 91.2%, the SE was 81.3%–96%, and the SP was 86.5%–92%. Among 2,588 vertebrae analyzed, 107 had mild and 49 had moderate or severe VFx by visual SQ grading. Per-vertebra analyses revealed good agreement, with k=0.580. Agreement between the methods tended to be highest in L1-L4 region. Agreement and validity measures were higher when only moderate and severe fractures were included. Conclusion The semi-automated quantitative vertebral morphometry measurements from CT lateral scout views provided good to excellent agreement with the standard SQ grading for assessment of

  3. Differences in cell morphometry, cell wall topography and gp70 expression correlate with the virulence of Sporothrix brasiliensis clinical isolates.

    PubMed

    Castro, Rafaela A; Kubitschek-Barreira, Paula H; Teixeira, Pedro A C; Sanches, Glenda F; Teixeira, Marcus M; Quintella, Leonardo P; Almeida, Sandro R; Costa, Rosane O; Camargo, Zoilo P; Felipe, Maria S S; de Souza, Wanderley; Lopes-Bezerra, Leila M

    2013-01-01

    Sporotrichosis is a chronic infectious disease affecting both humans and animals. For many years, this subcutaneous mycosis had been attributed to a single etiological agent; however, it is now known that this taxon consists of a complex of at least four pathogenic species, including Sporothrix schenckii and Sporothrix brasiliensis. Gp70 was previously shown to be an important antigen and adhesin expressed on the fungal cell surface and may have a key role in immunomodulation and host response. The aim of this work was to study the virulence, morphometry, cell surface topology and gp70 expression of clinical isolates of S. brasiliensis compared with two reference strains of S. schenckii. Several clinical isolates related to severe human cases or associated with the Brazilian zoonotic outbreak of sporotrichosis were genotyped and clustered as S. brasiliensis. Interestingly, in a murine subcutaneous model of sporotrichosis, these isolates showed a higher virulence profile compared with S. schenckii. A single S. brasiliensis isolate from an HIV-positive patient not only showed lower virulence but also presented differences in cell morphometry, cell wall topography and abundant gp70 expression compared with the virulent isolates. In contrast, the highly virulent S. brasiliensis isolates showed reduced levels of cell wall gp70. These observations were confirmed by the topographical location of the gp70 antigen using immunoelectromicroscopy in both species. In addition, the gp70 molecule was sequenced and identified using mass spectrometry, and the sequenced peptides were aligned into predicted proteins using Blastp with the S. schenckii and S. brasiliensis genomes.

  4. Genome-scale study reveals reduced metabolic adaptability in patients with non-alcoholic fatty liver disease.

    PubMed

    Hyötyläinen, Tuulia; Jerby, Livnat; Petäjä, Elina M; Mattila, Ismo; Jäntti, Sirkku; Auvinen, Petri; Gastaldelli, Amalia; Yki-Järvinen, Hannele; Ruppin, Eytan; Orešič, Matej

    2016-02-03

    Non-alcoholic fatty liver disease (NAFLD) is a major risk factor leading to chronic liver disease and type 2 diabetes. Here we chart liver metabolic activity and functionality in NAFLD by integrating global transcriptomic data, from human liver biopsies, and metabolic flux data, measured across the human splanchnic vascular bed, within a genome-scale model of human metabolism. We show that an increased amount of liver fat induces mitochondrial metabolism, lipolysis, glyceroneogenesis and a switch from lactate to glycerol as substrate for gluconeogenesis, indicating an intricate balance of exacerbated opposite metabolic processes in glycemic regulation. These changes were associated with reduced metabolic adaptability on a network level in the sense that liver fat accumulation puts increasing demands on the liver to adaptively regulate metabolic responses to maintain basic liver functions. We propose that failure to meet excessive metabolic challenges coupled with reduced metabolic adaptability may lead to a vicious pathogenic cycle leading to the co-morbidities of NAFLD.

  5. Genome-scale study reveals reduced metabolic adaptability in patients with non-alcoholic fatty liver disease

    PubMed Central

    Hyötyläinen, Tuulia; Jerby, Livnat; Petäjä, Elina M.; Mattila, Ismo; Jäntti, Sirkku; Auvinen, Petri; Gastaldelli, Amalia; Yki-Järvinen, Hannele; Ruppin, Eytan; Orešič, Matej

    2016-01-01

    Non-alcoholic fatty liver disease (NAFLD) is a major risk factor leading to chronic liver disease and type 2 diabetes. Here we chart liver metabolic activity and functionality in NAFLD by integrating global transcriptomic data, from human liver biopsies, and metabolic flux data, measured across the human splanchnic vascular bed, within a genome-scale model of human metabolism. We show that an increased amount of liver fat induces mitochondrial metabolism, lipolysis, glyceroneogenesis and a switch from lactate to glycerol as substrate for gluconeogenesis, indicating an intricate balance of exacerbated opposite metabolic processes in glycemic regulation. These changes were associated with reduced metabolic adaptability on a network level in the sense that liver fat accumulation puts increasing demands on the liver to adaptively regulate metabolic responses to maintain basic liver functions. We propose that failure to meet excessive metabolic challenges coupled with reduced metabolic adaptability may lead to a vicious pathogenic cycle leading to the co-morbidities of NAFLD. PMID:26839171

  6. [Differential diagnosis of reduced uptake images revealed by bone scan: about a case of acute lymphoblastic leukemia].

    PubMed

    Bahadi, Nisrine; Biyi, Abdelhamid; Oueriagli, Salah Nabih; Doudouh, Abderrahim

    2016-01-01

    If increased uptake during bone scan usually bring to light many bone pathologies, reduced uptakes are a rare occurrence and they require careful analysis to avoid erroneous interpretations. We report the case of a 17-year old admitted with diffuse bone pain, hypercalcemia and thrombopenia. Bone scan showed areas of low uptakes. Bone marrow tests allowed the diagnosis of acute lymphoblastic leukemia. This case report aims to discuss the main differential diagnoses based on such bone scan abnormalities.

  7. Ultrastructural and histochemical analysis reveals ethylene-induced responses underlying reduced peel collapse in detached citrus fruit.

    PubMed

    Cajuste, Jacques F; García-Breijo, Francisco J; Reig-Armiñana, José; Lafuente, María T

    2011-10-01

    Fruits from many citrus cultivars develop depressed areas in the flavedo (outer part of the peel) and albedo (inner part) following detachment. Although ultrastructural analysis may provide important information about multiple plant responses to stresses and external stimuli at the cell and tissue levels, and despite the proved efficacy of ethylene in reducing peel damage in citrus fruit, cytological responses of this horticultural crop to protective ethylene concentrations have not yet been reported. We show that applying high ethylene levels (2 μL L(-1) for 14 days) causes sublethal stress as it favored the alteration of cuticle, vacuole, middle lamella and primary wall, especially in the albedo cells, but reduced peel collapse in detached mature "Navelate" oranges (C. sinensis, L. Osbeck) held under nonstressful environmental conditions (22°C and 90-95% RH). Ethylene did not induce relevant changes in lignification but favored the deposition of pectic exudates and the release of sugars from degradation of cell polysaccharides including starch, cellulose, and pectins. In contrast, inhibiting ethylene perception by applying 1-methylcyclopropene (1-MCP) reduced these ethylene-related responses and favored degradation of cell membranes and peel damage. The overall results reflect that mature oranges tolerate high ethylene levels that might favor the activation of defense responses involving oxidative-stress related mechanisms and recycling of nutrients and carbon supply to enable cells to sustain respiration and cope with carbon deprivation stress caused by detachment.

  8. In Vivo Lung Morphometry with Accelerated Hyperpolarized 3He Diffusion MRI: A Preliminary Study

    PubMed Central

    Chang, Yulin V.; Quirk, James D.; Yablonskiy, Dmitriy A.

    2014-01-01

    Purpose Parallel imaging can be used to reduce imaging time and to increase the spatial coverage in hyperpolarized gas MRI of the lung. In this proof-of-concept study we investigate the effects of parallel imaging on the morphometric measurement of lung microstructure using diffusion MRI with hyperpolarized 3He. Methods Fully sampled and under-sampled multi-b diffusion data were acquired from human subjects using an 8-channel 3He receive coil. A parallel imaging reconstruction technique (GRAPPA) was used to reconstruct under-sampled k-space data. The morphometric results of the GRAPPA-reconstructed data were compared with the results of fully sampled data for three types of subjects: healthy volunteers, mild, and moderate COPD patients. Results Morphometric measurements varied only slightly at mild acceleration factors. The results were largely well preserved compared to fully sampled data for different lung conditions. Conclusion Parallel imaging, given sufficient signal-to-noise ratio, provides a reliable means to accelerate hyperpolarized-gas MRI with no significant difference in the measurement of lung morphometry from the fully sampled images. GRAPPA is a promising technique to significantly reduce imaging time and/or to improve the spatial coverage for the morphometric measurement with hyperpolarized gases. PMID:24799044

  9. Differential potassium channel gene regulation in BXD mice reveals novel targets for pharmacogenetic therapies to reduce heavy alcohol drinking.

    PubMed

    Rinker, Jennifer A; Fulmer, Diana B; Trantham-Davidson, Heather; Smith, Maren L; Williams, Robert W; Lopez, Marcelo F; Randall, Patrick K; Chandler, L Judson; Miles, Michael F; Becker, Howard C; Mulholland, Patrick J

    2017-02-01

    Alcohol (ethanol) dependence is a chronic relapsing brain disorder partially influenced by genetics and characterized by an inability to regulate harmful levels of drinking. Emerging evidence has linked genes that encode KV7, KIR, and KCa2 K(+) channels with variation in alcohol-related behaviors in rodents and humans. This led us to experimentally test relations between K(+) channel genes and escalation of drinking in a chronic-intermittent ethanol (CIE) exposure model of dependence in BXD recombinant inbred strains of mice. Transcript levels for K(+) channel genes in the prefrontal cortex (PFC) and nucleus accumbens (NAc) covary with voluntary ethanol drinking in a non-dependent cohort. Transcripts that encode KV7 channels covary negatively with drinking in non-dependent BXD strains. Using a pharmacological approach to validate the genetic findings, C57BL/6J mice were allowed intermittent access to ethanol to establish baseline consumption before they were treated with retigabine, an FDA-approved KV7 channel positive modulator. Systemic administration significantly reduced drinking, and consistent with previous evidence, retigabine was more effective at reducing voluntary consumption in high-drinking than low-drinking subjects. We evaluated the specific K(+) channel genes that were most sensitive to CIE exposure and identified a gene subset in the NAc and PFC that were dysregulated in the alcohol-dependent BXD cohort. CIE-induced modulation of nine genes in the NAc and six genes in the PFC covaried well with the changes in drinking induced by ethanol dependence. Here we identified novel candidate genes in the NAc and PFC that are regulated by ethanol dependence and correlate with voluntary drinking in non-dependent and dependent BXD mice. The findings that Kcnq expression correlates with drinking and that retigabine reduces consumption suggest that KV7 channels could be pharmacogenetic targets to treat individuals with alcohol addiction.

  10. Towards fast and routine analyses of volcanic ash morphometry for eruption surveillance applications

    NASA Astrophysics Data System (ADS)

    Leibrandt, Sébastien; Le Pennec, Jean-Luc

    2015-05-01

    The morphometry of volcanic ash produced by explosive eruptions yields ample information on fragmentation processes (e.g. magmatic vs magma-water interactions), and on transport and sedimentation mechanisms. Most previous works on volcanic clast morphometry focused on the Apparent (2D-)Projected shape of ASH grains, here termed APASH, to infer processes and eruptive styles. However, textural analyses of ash grains has remained a long and tedious task that made such approaches inappropriate for eruption surveillance duties. In this work we show that new technological advances on automated dispersion of granular materials imaged with a camera-coupled microscope and enhanced computer capabilities enable fast and high resolution image acquisition of thousands of ash grains that resolve this limitation. With a morpho-grainsizer designed for such fast and routine measurements we perform a series of APASH analyses on selected ash fractions of tephra deposits from known eruptive styles. We record the size, aspect ratio, circularity and convexity of APASH images and assess resolution, reproducibility, minimum population size, and total analytical duration, and offer recommendations for the reporting of APASH data for inter-laboratory comparisons. To avoid fractal geometry concerns, our analyses are carried out at constant size range (250-300 μm) and optical magnification (× 5) on ~ 3000 grains per samples collected from homogenized samples. Results from the andesitic 1999-ongoing eruption of Tungurahua volcano (Ecuador) show that ash particles from the moderate 2001 phase are relatively equant and convex in shape, while the stronger 2006 subplinian phase produced ash grains with more elongated, less circular and less convex APASH signatures. Ash grains from a basaltic scoria cone-forming eruption show even more ragged APASH characteristics. Overall, our protocol allows obtaining accurate and reproducible morphometric measurements that reveal subtle variations of the

  11. Towards fast and routine analyses of volcanic ash morphometry for eruption surveillance applications

    NASA Astrophysics Data System (ADS)

    Leibrandt, Sébastien; Le Pennec, Jean-Luc

    2015-04-01

    The morphometry of volcanic ash produced by explosive eruptions yields ample information on fragmentation processes (e.g. magmatic vs magma-water interactions), and on transport and sedimentation mechanisms. Most previous works on volcanic clast morphometry focused on the Apparent (2D-)Projected shape of ASH grains, here called APASH, to infer processes and eruptive styles. However, textural analyses of ash grains has remained a long and tedious task that made such approaches inappropriate for eruption surveillance duties. In this work we show that new technological advances on automated dispersion of granular materials imaged with a camera-coupled microscope and enhanced computer capabilities enable fast and high resolution image acquisition of thousands of ash grains that solve this limitation. With a morpho-grainsizer designed for such fast and routine measurements we perform a series of APASH analyses on selected ash fractions of tephra deposits from known eruptive styles. We record the size, aspect ratio, circularity and convexity of APASH images and assess resolution, reproducibility, minimum population size, and total analytical duration, and offer recommendations for the reporting of APASH data for interlaboratory comparisons. To avoid fractal geometry concerns, our analyses are carried out at constant size range (250-300 um) and optical magnification (x5) on ~3000 grains/samples collected from homogenized samples. Results from the andesitic 1999-ongoing eruption of Tungurahua volcano (Ecuador) show that ash particles from the moderate 2001 phase are relatively equant and convex in shape, while the stronger 2006 subplinian phase produced ash grains with more elongated, less circular and less convex APASH signatures. Ash grains from a basaltic scoria cone-forming eruption show even more ragged APASH characteristics. Overall, our protocol allows obtaining accurate and reproducible morphometric measurements that reveal subtle variations of the morphological

  12. Effects of reduced natural background radiation on Drosophila melanogaster growth and development as revealed by the FLYINGLOW program.

    PubMed

    Morciano, Patrizia; Iorio, Roberto; Iovino, Daniela; Cipressa, Francesca; Esposito, Giuseppe; Porrazzo, Antonella; Satta, Luigi; Alesse, Edoardo; Tabocchini, Maria Antonella; Cenci, Giovanni

    2018-01-01

    Natural background radiation of Earth and cosmic rays played a relevant role during the evolution of living organisms. However, how chronic low doses of radiation can affect biological processes is still unclear. Previous data have indicated that cells grown at the Gran Sasso Underground Laboratory (LNGS, L'Aquila) of National Institute of Nuclear Physics (INFN) of Italy, where the dose rate of cosmic rays and neutrons is significantly reduced with respect to the external environment, elicited an impaired response against endogenous damage as compared to cells grown outside LNGS. This suggests that environmental radiation contributes to the development of defense mechanisms at cellular level. To further understand how environmental radiation affects metabolism of living organisms, we have recently launched the FLYINGLOW program that aims at exploiting Drosophila melanogaster as a model for evaluating the effects of low doses/dose rates of radiation at the organismal level. Here, we will present a comparative data set on lifespan, motility and fertility from different Drosophila strains grown in parallel at LNGS and in a reference laboratory at the University of L'Aquila. Our data suggest the reduced radiation environment can influence Drosophila development and, depending on the genetic background, may affect viability for several generations even when flies are moved back to normal background radiation. As flies are considered a valuable model for human biology, our results might shed some light on understanding the effect of low dose radiation also in humans. © 2017 Wiley Periodicals, Inc.

  13. A global database of volcano edifice morphometry using SRTM DEMs

    NASA Astrophysics Data System (ADS)

    Grosse, P.; van Wyk de Vries, B.; Petrinovic, I. A.; Euillades, P. A.

    2009-12-01

    The morphometry of volcanic edifices reflects the aggradational and degradational processes that interact during their evolution. In association with VOGRIPA, a global risk identification project, we are currently constructing a database on the morphometry of volcanic edifices using digital elevation models (DEMs) from the Shuttle Radar Topography Mission (SRTM). Our aim is to compile and make available a global database of morphometric parameters that characterize the shape and size of volcanic edifices. The 90-meter SRTM DEM is presently the best public-access DEM dataset for this task because of its near-global coverage and spatial resolution that is high enough for the analysis of composite volcanic edifices. The Smithsonian Institution database lists 1536 active/potentially active volcanoes worldwide. Of these, ~900 volcano edifices can be analyzed with the SRTM DEMs, discarding volcanoes not covered by the dataset above latitudes 60°N and 56°S, submarine volcanoes, volcanoes with mostly negative topographies (i.e. calderas, maars) and monogenetic cones and domes, which are too small to accurately study with the 90-meter resolution. Morphometric parameters are acquired using an expressly written IDL-language code named MORVOLC. Edifice outline is determined via a semi-automated algorithm that identifies slope-breaks between user-estimated maximum and minimum outlines. Thus, volcanic edifices as topographic entities are considered, excluding aprons or ring plains and other far-reaching volcanic products. Several morphometric parameters are computed which characterize edifice size and shape. Size parameters are height (from base to summit), volume, base and summit areas and widths (average, minimum, maximum). Plan shape is summarized using two independent dimensionless indexes that describe the shape of the elevation contours, ellipticity (quantifies the elongation of each contour) and irregularity (quantifies the irregularity or complexity of each contour

  14. Fast, automated measurement of nematode swimming (thrashing) without morphometry.

    PubMed

    Buckingham, Steven D; Sattelle, David B

    2009-07-20

    The "thrashing assay", in which nematodes are placed in liquid and the frequency of lateral swimming ("thrashing") movements estimated, is a well-established method for measuring motility in the genetic model organism Caenorhabditis elegans as well as in parasitic nematodes. It is used as an index of the effects of drugs, chemicals or mutations on motility and has proved useful in identifying mutants affecting behaviour. However, the method is laborious, subject to experimenter error, and therefore does not permit high-throughput applications. Existing automation methods usually involve analysis of worm shape, but this is computationally demanding and error-prone. Here we present a novel, robust and rapid method of automatically counting the thrashing frequency of worms that avoids morphometry but nonetheless gives a direct measure of thrashing frequency. Our method uses principal components analysis to remove the background, followed by computation of a covariance matrix of the remaining image frames from which the interval between statistically-similar frames is estimated. We tested the performance of our covariance method in measuring thrashing rates of worms using mutations that affect motility and found that it accurately substituted for laborious, manual measurements over a wide range of thrashing rates. The algorithm used also enabled us to determine a dose-dependent inhibition of thrashing frequency by the anthelmintic drug, levamisole, illustrating the suitability of the system for assaying the effects of drugs and chemicals on motility. Furthermore, the algorithm successfully measured the actions of levamisole on a parasitic nematode, Haemonchus contortus, which undergoes complex contorted shapes whilst swimming, without alterations in the code or of any parameters, indicating that it is applicable to different nematode species, including parasitic nematodes. Our method is capable of analyzing a 30 s movie in less than 30 s and can therefore be deployed

  15. The correlation between gray matter volume and perceived social support: a voxel-based morphometry study.

    PubMed

    Che, XianWei; Wei, DongTao; Li, WenFu; Li, HaiJiang; Qiao, Lei; Qiu, Jiang; Zhang, QingLin; Liu, YiJun

    2014-01-01

    Social support refers to interpersonal exchanges that include the combinations of aid, affirmation and affection. Perceived social support is a kind of subjective judgment of one's availability of social support. In spite of the importance of perceived social support to health, however, its neural substrate remains unknown. To address this question, voxel-based morphometry was employed to investigate the neural bases of individual differences in responses to the Perceived Social Support Scale (PSSS) in healthy volunteers (144 men and 203 women; mean age = 19.9; SD = 1.33, age range : 17-27). As a result, multiple regression analysis revealed that the PSSS scores were significantly and positively correlated with gray matter volume in a cluster that mainly included areas in posterior parts of posterior cingulate cortex, bilateral lingual cortex, left occipital lobe and cuneus. Highly-supported individuals had larger gray matter volume in these brain regions, implying a relatively high level of ability to engage in self-referential processes and social cognition. Our results provide a biological basis for exploring perceived social support particularly in relationship to various health parameters and outcomes.

  16. Using deep belief network modelling to characterize differences in brain morphometry in schizophrenia

    NASA Astrophysics Data System (ADS)

    Pinaya, Walter H. L.; Gadelha, Ary; Doyle, Orla M.; Noto, Cristiano; Zugman, André; Cordeiro, Quirino; Jackowski, Andrea P.; Bressan, Rodrigo A.; Sato, João R.

    2016-12-01

    Neuroimaging-based models contribute to increasing our understanding of schizophrenia pathophysiology and can reveal the underlying characteristics of this and other clinical conditions. However, the considerable variability in reported neuroimaging results mirrors the heterogeneity of the disorder. Machine learning methods capable of representing invariant features could circumvent this problem. In this structural MRI study, we trained a deep learning model known as deep belief network (DBN) to extract features from brain morphometry data and investigated its performance in discriminating between healthy controls (N = 83) and patients with schizophrenia (N = 143). We further analysed performance in classifying patients with a first-episode psychosis (N = 32). The DBN highlighted differences between classes, especially in the frontal, temporal, parietal, and insular cortices, and in some subcortical regions, including the corpus callosum, putamen, and cerebellum. The DBN was slightly more accurate as a classifier (accuracy = 73.6%) than the support vector machine (accuracy = 68.1%). Finally, the error rate of the DBN in classifying first-episode patients was 56.3%, indicating that the representations learned from patients with schizophrenia and healthy controls were not suitable to define these patients. Our data suggest that deep learning could improve our understanding of psychiatric disorders such as schizophrenia by improving neuromorphometric analyses.

  17. Normozoospermic versus teratozoospermic domestic cats: differential testicular volume, sperm morphometry, and subpopulation structure during epididymal maturation

    PubMed Central

    Gutiérrez-Reinoso, Miguel Angel; García-Herreros, Manuel

    2016-01-01

    Teratozoospermia (<40% morphologically normal spermatozoa/ejaculate) is a frequent phenomenon in feline species. This research was carried out to study the possible differences in testicular volume, differential sperm morphometric traits, and potential differences regarding the sperm subpopulational structure during epididymal sperm maturation in teratozoospermic feline donors. Epididymal sperm samples were collected from the caput (R1), corpus (R2), and cauda (R3) epididymidis in two donor groups (N: normozoospermic; T: teratozoospermic). Aliquots were assessed for concentration, viability, motility, and acrosomal integrity. Sperm morphometric descriptors from CASA-Morph analysis were analyzed by the Principal Component Analysis (PCA) and clustering analyses. Irrespective of the group analyzed, PCA revealed two Principal Components (PCs) for each epididymal region explaining more than the 93% of the variance. Surprisingly, the number of subpopulations remained constant in regions R1-R2-R3 irrespective of the donor group analyzed. However, the distribution of these subpopulations was found to be structurally different and strongly influenced by the epididymal region and the donor group. In conclusion, testicular morphometry and the sperm subpopulation structure were different in N and T donors. The alterations in subpopulations during epididymal maturation could be used as a potential clinical indicator of teratozoospermic individuals since an important influence of teratozoospermia on sperm subpopulation structure has been demonstrated. PMID:27624990

  18. Nuclear morphometry and molecular biomarkers of actinic keratosis, sun-damaged, and nonexposed skin.

    PubMed

    Carpenter, Philip M; Linden, Kenneth G; McLaren, Christine E; Li, Kuo-Tung; Arain, Shehla; Barr, Ronald J; Hite, Pamela; Sun, Joannie D; Meyskens, Frank L

    2004-12-01

    Computer-assisted image analysis is useful for quantifying the histologic and molecular changes of sun-induced squamous cell carcinoma progression. We used the CAS 200 image analysis system to measure nuclear morphometric parameters, p53 expression, and proliferation markers in actinic keratosis (AK), sun-exposed, and normal skin in 51 patients. Nuclear morphometry revealed significant increases in nuclear absorbance, irregularity of nuclear shape, and nuclear size in AK compared with normal and sun-damaged skin. These parameters showed significantly greater variability in AK nuclei. Argyrophyllic nucleolar organizer area and number were also significantly greater in AK compared with sun-damaged skin and normal skin. Ki67 and p53 expressions were both increased in sun-damaged skin relative to normal and greater still in AK. These data are evidence that sun damage induces proliferation and p53 abnormalities before the appearance of nuclear abnormalities and their associated DNA instability. Following these changes during a skin cancer chemopreventative trial can then help assess the efficacy of the agent and help determine where in the progression of neoplastic changes it exerts its biological effects.

  19. Grey matter volume alterations in CADASIL: a voxel-based morphometry study.

    PubMed

    Rossi Espagnet, Maria Camilla; Romano, Andrea; Carducci, Filippo; Calabria, Luigi Fausto; Fiorillo, Martina; Orzi, Francesco; Bozzao, Alessandro

    2012-04-01

    CADASIL is a hereditary disease characterized by cerebral subcortical microangiopathy leading to early onset cerebral strokes and progressive severe cognitive impairment. Until now, only few studies have investigated the extent and localization of grey matter (GM) involvement. The purpose of our study was to evaluate GM volume alterations in CADASIL patients compared to healthy subjects. We also looked for correlations between global and regional white matter (WM) lesion load and GM volume alterations. 14 genetically proved CADASIL patients and 12 healthy subjects were enrolled in our study. Brain MRI (1.5 T) was acquired in all subjects. Optimized-voxel based morphometry method was applied for the comparison of brain volumes between CADASIL patients and controls. Global and lobar WM lesion loads were calculated for each patient and used as covariate-of-interest for regression analyses with SPM-8. Compared to controls, patients showed GM volume reductions in bilateral temporal lobes (p < 0.05; FDR-corrected). Regression analysis in the patient group revealed a correlation between total WM lesion load and temporal GM atrophy (p < 0.05; uncorrected), not between temporal lesion load and GM atrophy. Temporal GM volume reduction was demonstrated in CADASIL patients compared to controls; it was related to WM lesion load involving the whole brain but not to lobar and, specifically, temporal WM lesion load. Complex interactions between sub-cortical and cortical damage should be hypothesized.

  20. Morphology, morphometry and ultrastructure of captive six-banded armadillo (Euphractus sexcinctus) sperm.

    PubMed

    Sousa, P C; Santos, E A A; Bezerra, J A B; Lima, G L; Castelo, T S; Fontenele-Neto, J D; Silva, A R

    2013-08-01

    We analyzed the sperm characteristics of captive six-banded armadillos (Euphractus sexcinctus), by the assessment of sperm morphology, morphometry, and ultrastructure. In general, armadillo's ejaculates present more than 80% of sperm within the range considered normal for sperm morphology currently accepted for other mammals. Coiled tails (3.9%) and detached heads (2.8%) were the defects most frequently verified. The morphometric analysis revealed that the total length of six-banded armadillo sperm is 77.6±1.2μm, and the length of the tail is 64.7±1.1μm on average. They also present a big head that corresponds to 16.6% of the entire sperm. Through transmission electron microscopy, we identified the presence of electron lucent points into the nucleus and the presence of about 45 mitochondria spirals in the mitochondrial sheath midpiece as a peculiarity of the six-banded armadillo sperm. Copyright © 2013 Elsevier B.V. All rights reserved.

  1. Exploring the effects of acid mine drainage on diatom teratology using geometric morphometry.

    PubMed

    Olenici, Adriana; Blanco, Saúl; Borrego-Ramos, María; Momeu, Laura; Baciu, Călin

    2017-07-11

    Metal pollution of aquatic habitats is a major and persistent environmental problem. Acid mine drainage (AMD) affects lotic systems in numerous and interactive ways. In the present work, a mining area (Roșia Montană) was chosen as study site, and we focused on two aims: (i) to find the set of environmental predictors leading to the appearance of the abnormal diatom individuals in the study area and (ii) to assess the relationship between the degree of valve outline deformation and AMD-derived pollution. In this context, morphological differences between populations of Achnanthidium minutissimum and A. macrocephalum, including normal and abnormal individuals, were evidenced by means of valve shape analysis. Geometric morphometry managed to capture and discriminate normal and abnormal individuals. Multivariate analyses (NMDS, PLS) separated the four populations of the two species mentioned and revealed the main physico-chemical parameters that influenced valve deformation in this context, namely conductivity, Zn, and Cu. ANOSIM test evidenced the presence of statistically significant differences between normal and abnormal individuals within both chosen Achnanthidium taxa. In order to determine the relative contribution of each of the measured physico-chemical parameters in the observed valve outline deformations, a PLS was conducted, confirming the results of the NMDS. The presence of deformed individuals in the study area can be attributed to the fact that the diatom communities were strongly affected by AMD released from old mining works and waste rock deposits.

  2. The pterygoalar bar: A meta-analysis of its prevalence, morphology and morphometry.

    PubMed

    Pękala, Przemysław A; Henry, Brandon Michael; Pękala, Jakub R; Frączek, Paulina A; Taterra, Dominik; Natsis, Konstantinos; Piagkou, Maria; Skrzat, Janusz; Tomaszewska, Iwona M

    2017-09-01

    The pterygoalar (PA) bar is a bony bridge resulting from the partial or complete ossification of a PA ligament. The aim of this meta-analysis was to systematically analyze and provide the most comprehensive data on the prevalence, morphology and topographical anatomy of the PA bar. A comprehensive search of the major electronic databases (PubMed, Embase, ScienceDirect, SciELO, BIOSIS, and Web of Science) was conducted in order to identify relevant studies. Studies reporting the prevalence, side of occurrence, gender dimorphism and morphometry of the PA bar were included in the current study. A total of 25 articles (n = 16,168 subjects) were included in the meta-analysis. The overall pooled prevalence of the complete PA bar was 4.4% (95% CI: 3.0-6.0) and of the incomplete was 8.4% (95% CI: 4.6-13.3). The PA bar was most often observed unilaterally, on the left side. Analysis of geographical subgroups revealed considerable differences, with the lowest prevalence rates in Europe for both incomplete and complete PA bars. Considering the prevalence and anatomical characteristics of the PA bar, caution is recommended while planning or performing transfacial needle approach to the foramen ovale and when considering a differential diagnosis for nerve compression or entrapment syndromes. Copyright © 2017 European Association for Cranio-Maxillo-Facial Surgery. Published by Elsevier Ltd. All rights reserved.

  3. The application of control charts to determine the effect of grid cell size on landform morphometry

    NASA Astrophysics Data System (ADS)

    Napieralski, Jacob; Nalepa, Nick

    2010-02-01

    Geoscientists have become increasingly dependent on digital elevation models (DEMs) to delineate and measure landforms and landscapes. However, the DEM grid cell size available may not be the optimum resolution; this can mask subtle changes in measurements and lead to erroneous results. This paper presents a standardized statistical technique (i.e. statistical process control charts (SPCC)) for determining the optimum DEM resolution (i.e. the coarsest resolution in which detail is not sacrificed) for landforms (e.g. drumlins). For this study, forty-four DEM resolutions, ranging from 1 to 80 m, were used to assess the effect of resolution on drumlin size, shape, and centroid. The results indicate that the optimum resolution for the size variables (width and length) was coarser than the optimum resolution for shape indices (elongation and rose curve). Drumlin location tends to drift in a predictable direction and rate as grid cell size coarsens above particular thresholds. The results prove that resolution plays a critical role in correctly evaluating drumlin morphometry and that care must be taken when utilizing DEMs to summarize drumlin characteristics. The creation of a standardized technique to describe drumlins will allow for scrutiny of previous work and straightforward comparative analyses between studies, while utilizing the optimum resolution will help decipher landform patterns, reveal relationships, and provide more insight into landform evolution.

  4. Using deep belief network modelling to characterize differences in brain morphometry in schizophrenia

    PubMed Central

    Pinaya, Walter H. L.; Gadelha, Ary; Doyle, Orla M.; Noto, Cristiano; Zugman, André; Cordeiro, Quirino; Jackowski, Andrea P.; Bressan, Rodrigo A.; Sato, João R.

    2016-01-01

    Neuroimaging-based models contribute to increasing our understanding of schizophrenia pathophysiology and can reveal the underlying characteristics of this and other clinical conditions. However, the considerable variability in reported neuroimaging results mirrors the heterogeneity of the disorder. Machine learning methods capable of representing invariant features could circumvent this problem. In this structural MRI study, we trained a deep learning model known as deep belief network (DBN) to extract features from brain morphometry data and investigated its performance in discriminating between healthy controls (N = 83) and patients with schizophrenia (N = 143). We further analysed performance in classifying patients with a first-episode psychosis (N = 32). The DBN highlighted differences between classes, especially in the frontal, temporal, parietal, and insular cortices, and in some subcortical regions, including the corpus callosum, putamen, and cerebellum. The DBN was slightly more accurate as a classifier (accuracy = 73.6%) than the support vector machine (accuracy = 68.1%). Finally, the error rate of the DBN in classifying first-episode patients was 56.3%, indicating that the representations learned from patients with schizophrenia and healthy controls were not suitable to define these patients. Our data suggest that deep learning could improve our understanding of psychiatric disorders such as schizophrenia by improving neuromorphometric analyses. PMID:27941946

  5. Morphometry of eyes, antennae and wings in three species of Siagona(Coleoptera, Carabidae)

    PubMed Central

    Talarico, Federica; Brandmayr, Pietro; Giglio, Anita; Massolo, Alessandro; Brandmayr, Tullia Zetto

    2011-01-01

    Abstract In carabid beetles, physiological and behavioural characteristics reflect specific habitat demands and there is a strong correlation between body form and habit in species with different life style. In this study, we compared the morphometry and compound eye characteristics of three species of the genus Siagona: Siagona jenissoni, Siagona dejeani and Siagona europaea. These carabids have a stenotopic lifestyle in Mediterranean clayey soils, inhabiting the ground fissure system formed during the dry season. All species have a Mediterranean distribution and are nocturnal olfactory hunters, and are strict ant predators. For morphometric measurements, we considered body length (mm), wing length (mm), antenna length (mm), head width (mm), trochanter length (mm), number of ommatidia, eye surface area (mm2), ommatidia density (number of ommatidia/mm2 of eye surface area), head height (mm), thorax height (mm) and abdomen height (mm). The data revealed intersexual and interspecific differences. The three species differ in relative length of the antennae, density and number of ommatidia and relative trochanter length. Significant differences occurred in wing sizes, which are well developed in Siagona europaea, the only species capable of flight. When eye size is compared with other ground beetles of various lifestyles, Siagona shows pronounced “microphthalmy” an adaptation to subterranean life in clayey crevices of tropical and subtropical climates with a marked dry season. PMID:21738413

  6. Detecting Brain Growth Patterns in Normal Children using Tensor-Based Morphometry

    PubMed Central

    Hua, Xue; Leow, Alex D.; Levitt, Jennifer G.; Caplan, Rochelle; Thompson, Paul M.; Toga, Arthur W.

    2010-01-01

    Previous magnetic resonance imaging (MRI)-based volumetric studies have shown age-related increases in the volume of total white matter and decreases in the volume of total gray matter of normal children. Recent adaptations of image analysis strategies enable the detection of human brain growth with improved spatial resolution. In this article, we further explore the spatio-temporal complexity of adolescent brain maturation with tensor-based morphometry. By utilizing a novel non-linear elastic intensity-based registration algorithm on the serial structural MRI scans of 13 healthy children, individual Jacobian growth maps are generated and then registered to a common anatomical space. Statistical analyses reveal significant tissue growth in cerebral white matter, contrasted with gray matter loss in parietal, temporal, and occipital lobe. In addition, a linear regression with age and gender suggests a slowing down of the growth rate in regions with the greatest white matter growth. We demonstrate that a tensor-based Jacobian map is a sensitive and reliable method to detect regional tissue changes during development. PMID:18064588

  7. X-ray Crystallography Reveals a Reduced Substrate Complex of UDP-Galactopyranose Mutase Poised for Covalent Catalysis by Flavin

    SciTech Connect

    Gruber, Todd D.; Westler, William M.; Kiessling, Laura L.; Forest, Katrina T.

    2009-11-04

    The flavoenzyme uridine 5'-diphosphate galactopyranose mutase (UGM or Glf) catalyzes the interconversion of UDP-galactopyranose and UDP-galactofuranose. The latter is a key building block for cell wall construction in numerous pathogens, including Mycobacterium tuberculosis. Mechanistic studies of UGM suggested a novel role for the flavin, and we previously provided evidence that the catalytic mechanism proceeds through a covalent flavin-galactose iminium. Here, we describe 2.3 and 2.5 {angstrom} resolution X-ray crystal structures of the substrate-bound enzyme in oxidized and reduced forms, respectively. In the latter, C1 of the substrate is 3.6 {angstrom} from the nucleophilic flavin N5 position. This orientation is consistent with covalent catalysis by flavin.

  8. Altered pre-reflective sense of agency in autism spectrum disorders as revealed by reduced intentional binding.

    PubMed

    Sperduti, Marco; Pieron, Marie; Leboyer, Marion; Zalla, Tiziana

    2014-02-01

    Autism spectrum disorders (ASDs) are neurodevelopmental conditions that severely affect social interaction, communication and several behavioural and cognitive functions, such as planning and monitoring motor actions. A renewed interest in intrapersonal cognition has recently emerged suggesting a putative dissociation between impaired declarative processes, such as autobiographical memory, and spared implicit processes, such as the sense of agency (SoA) in ASDs. However, so far only a few studies have investigated the integrity of SoA using tasks exclusively tapping reflective mechanisms. Since pre-reflective processes of SoA are based on the same predictive internal models that are involved in planning and monitoring actions, we hypothesized that pre-reflective aspects of SoA, as measured by the intentional binding effect, would be altered in adults with high functioning autism spectrum disorders, relative to volunteers with typical development. Here, in accordance with our hypothesis, we report reduced IB in participants with ASDs.

  9. Higher Dimensional Meta-State Analysis Reveals Reduced Resting fMRI Connectivity Dynamism in Schizophrenia Patients

    PubMed Central

    Miller, Robyn L.; Yaesoubi, Maziar; Turner, Jessica A.; Mathalon, Daniel; Preda, Adrian; Pearlson, Godfrey; Adali, Tulay; Calhoun, Vince D.

    2016-01-01

    Resting-state functional brain imaging studies of network connectivity have long assumed that functional connections are stationary on the timescale of a typical scan. Interest in moving beyond this simplifying assumption has emerged only recently. The great hope is that training the right lens on time-varying properties of whole-brain network connectivity will shed additional light on previously concealed brain activation patterns characteristic of serious neurological or psychiatric disorders. We present evidence that multiple explicitly dynamical properties of time-varying whole-brain network connectivity are strongly associated with schizophrenia, a complex mental illness whose symptomatic presentation can vary enormously across subjects. As with so much brain-imaging research, a central challenge for dynamic network connectivity lies in determining transformations of the data that both reduce its dimensionality and expose features that are strongly predictive of important population characteristics. Our paper introduces an elegant, simple method of reducing and organizing data around which a large constellation of mutually informative and intuitive dynamical analyses can be performed. This framework combines a discrete multidimensional data-driven representation of connectivity space with four core dynamism measures computed from large-scale properties of each subject’s trajectory, ie., properties not identifiable with any specific moment in time and therefore reasonable to employ in settings lacking inter-subject time-alignment, such as resting-state functional imaging studies. Our analysis exposes pronounced differences between schizophrenia patients (Nsz = 151) and healthy controls (Nhc = 163). Time-varying whole-brain network connectivity patterns are found to be markedly less dynamically active in schizophrenia patients, an effect that is even more pronounced in patients with high levels of hallucinatory behavior. To the best of our knowledge this is

  10. Higher Dimensional Meta-State Analysis Reveals Reduced Resting fMRI Connectivity Dynamism in Schizophrenia Patients.

    PubMed

    Miller, Robyn L; Yaesoubi, Maziar; Turner, Jessica A; Mathalon, Daniel; Preda, Adrian; Pearlson, Godfrey; Adali, Tulay; Calhoun, Vince D

    2016-01-01

    Resting-state functional brain imaging studies of network connectivity have long assumed that functional connections are stationary on the timescale of a typical scan. Interest in moving beyond this simplifying assumption has emerged only recently. The great hope is that training the right lens on time-varying properties of whole-brain network connectivity will shed additional light on previously concealed brain activation patterns characteristic of serious neurological or psychiatric disorders. We present evidence that multiple explicitly dynamical properties of time-varying whole-brain network connectivity are strongly associated with schizophrenia, a complex mental illness whose symptomatic presentation can vary enormously across subjects. As with so much brain-imaging research, a central challenge for dynamic network connectivity lies in determining transformations of the data that both reduce its dimensionality and expose features that are strongly predictive of important population characteristics. Our paper introduces an elegant, simple method of reducing and organizing data around which a large constellation of mutually informative and intuitive dynamical analyses can be performed. This framework combines a discrete multidimensional data-driven representation of connectivity space with four core dynamism measures computed from large-scale properties of each subject's trajectory, ie., properties not identifiable with any specific moment in time and therefore reasonable to employ in settings lacking inter-subject time-alignment, such as resting-state functional imaging studies. Our analysis exposes pronounced differences between schizophrenia patients (Nsz = 151) and healthy controls (Nhc = 163). Time-varying whole-brain network connectivity patterns are found to be markedly less dynamically active in schizophrenia patients, an effect that is even more pronounced in patients with high levels of hallucinatory behavior. To the best of our knowledge this is the

  11. Cultivation of a human-associated TM7 phylotype reveals a reduced genome and epibiotic parasitic lifestyle

    PubMed Central

    He, Xuesong; McLean, Jeffrey S.; Edlund, Anna; Yooseph, Shibu; Hall, Adam P.; Liu, Su-Yang; Dorrestein, Pieter C.; Esquenazi, Eduardo; Hunter, Ryan C.; Cheng, Genhong; Nelson, Karen E.; Lux, Renate; Shi, Wenyuan

    2015-01-01

    The candidate phylum TM7 is globally distributed and often associated with human inflammatory mucosal diseases. Despite its prevalence, the TM7 phylum remains recalcitrant to cultivation, making it one of the most enigmatic phyla known. In this study, we cultivated a TM7 phylotype (TM7x) from the human oral cavity. This extremely small coccus (200–300 nm) has a distinctive lifestyle not previously observed in human-associated microbes. It is an obligate epibiont of an Actinomyces odontolyticus strain (XH001) yet also has a parasitic phase, thereby killing its host. This first completed genome (705 kb) for a human-associated TM7 phylotype revealed a complete lack of amino acid biosynthetic capacity. Comparative genomics analyses with uncultivated environmental TM7 assemblies show remarkable conserved gene synteny and only minimal gene loss/gain that may have occurred as TM7x adapted to conditions within the human host. Transcriptomic and metabolomic profiles provided the first indications, to our knowledge, that there is signaling interaction between TM7x and XH001. Furthermore, the induction of TNF-α production in macrophages by XH001 was repressed in the presence of TM7x, suggesting its potential immune suppression ability. Overall, our data provide intriguing insights into the uncultivability, pathogenicity, and unique lifestyle of this previously uncharacterized oral TM7 phylotype. PMID:25535390

  12. Cultivation of a human-associated TM7 phylotype reveals a reduced genome and epibiotic parasitic lifestyle.

    PubMed

    He, Xuesong; McLean, Jeffrey S; Edlund, Anna; Yooseph, Shibu; Hall, Adam P; Liu, Su-Yang; Dorrestein, Pieter C; Esquenazi, Eduardo; Hunter, Ryan C; Cheng, Genhong; Nelson, Karen E; Lux, Renate; Shi, Wenyuan

    2015-01-06

    The candidate phylum TM7 is globally distributed and often associated with human inflammatory mucosal diseases. Despite its prevalence, the TM7 phylum remains recalcitrant to cultivation, making it one of the most enigmatic phyla known. In this study, we cultivated a TM7 phylotype (TM7x) from the human oral cavity. This extremely small coccus (200-300 nm) has a distinctive lifestyle not previously observed in human-associated microbes. It is an obligate epibiont of an Actinomyces odontolyticus strain (XH001) yet also has a parasitic phase, thereby killing its host. This first completed genome (705 kb) for a human-associated TM7 phylotype revealed a complete lack of amino acid biosynthetic capacity. Comparative genomics analyses with uncultivated environmental TM7 assemblies show remarkable conserved gene synteny and only minimal gene loss/gain that may have occurred as TM7x adapted to conditions within the human host. Transcriptomic and metabolomic profiles provided the first indications, to our knowledge, that there is signaling interaction between TM7x and XH001. Furthermore, the induction of TNF-α production in macrophages by XH001 was repressed in the presence of TM7x, suggesting its potential immune suppression ability. Overall, our data provide intriguing insights into the uncultivability, pathogenicity, and unique lifestyle of this previously uncharacterized oral TM7 phylotype.

  13. Polymorphism Analysis Reveals Reduced Negative Selection and Elevated Rate of Insertions and Deletions in Intrinsically Disordered Protein Regions.

    PubMed

    Khan, Tahsin; Douglas, Gavin M; Patel, Priyenbhai; Nguyen Ba, Alex N; Moses, Alan M

    2015-06-04

    Intrinsically disordered protein regions are abundant in eukaryotic proteins and lack stable tertiary structures and enzymatic functions. Previous studies of disordered region evolution based on interspecific alignments have revealed an increased propensity for indels and rapid rates of amino acid substitution. How disordered regions are maintained at high abundance in the proteome and across taxa, despite apparently weak evolutionary constraints, remains unclear. Here, we use single nucleotide and indel polymorphism data in yeast and human populations to survey the population variation within disordered regions. First, we show that single nucleotide polymorphisms in disordered regions are under weaker negative selection compared with more structured protein regions and have a higher proportion of neutral non-synonymous sites. We also confirm previous findings that nonframeshifting indels are much more abundant in disordered regions relative to structured regions. We find that the rate of nonframeshifting indel polymorphism in intrinsically disordered regions resembles that of noncoding DNA and pseudogenes, and that large indels segregate in disordered regions in the human population. Our survey of polymorphism confirms patterns of evolution in disordered regions inferred based on longer evolutionary comparisons.

  14. Polymorphism Analysis Reveals Reduced Negative Selection and Elevated Rate of Insertions and Deletions in Intrinsically Disordered Protein Regions

    PubMed Central

    Khan, Tahsin; Douglas, Gavin M.; Patel, Priyenbhai; Nguyen Ba, Alex N.; Moses, Alan M.

    2015-01-01

    Intrinsically disordered protein regions are abundant in eukaryotic proteins and lack stable tertiary structures and enzymatic functions. Previous studies of disordered region evolution based on interspecific alignments have revealed an increased propensity for indels and rapid rates of amino acid substitution. How disordered regions are maintained at high abundance in the proteome and across taxa, despite apparently weak evolutionary constraints, remains unclear. Here, we use single nucleotide and indel polymorphism data in yeast and human populations to survey the population variation within disordered regions. First, we show that single nucleotide polymorphisms in disordered regions are under weaker negative selection compared with more structured protein regions and have a higher proportion of neutral non-synonymous sites. We also confirm previous findings that nonframeshifting indels are much more abundant in disordered regions relative to structured regions. We find that the rate of nonframeshifting indel polymorphism in intrinsically disordered regions resembles that of noncoding DNA and pseudogenes, and that large indels segregate in disordered regions in the human population. Our survey of polymorphism confirms patterns of evolution in disordered regions inferred based on longer evolutionary comparisons. PMID:26047845

  15. Preclinical evaluation of nuclear morphometry and tissue topology for breast carcinoma detection and margin assessment.

    PubMed

    Nyirenda, Ndeke; Farkas, Daniel L; Ramanujan, V Krishnan

    2011-04-01

    Prevention and early detection of breast cancer are the major prophylactic measures taken to reduce the breast cancer related mortality and morbidity. Clinical management of breast cancer largely relies on the efficacy of the breast-conserving surgeries and the subsequent radiation therapy. A key problem that limits the success of these surgeries is the lack of accurate, real-time knowledge about the positive tumor margins in the surgically excised tumors in the operating room. This leads to tumor recurrence and, hence, the need for repeated surgeries. Current intraoperative techniques such as frozen section pathology or touch imprint cytology severely suffer from poor sampling and non-optimal detection sensitivity. Even though histopathology analysis can provide information on positive tumor margins post-operatively (~2-3 days), this information is of no immediate utility in the operating rooms. In this article, we propose a novel image analysis method for tumor margin assessment based on nuclear morphometry and tissue topology and demonstrate its high sensitivity/specificity in preclinical animal model of breast carcinoma. The method relies on imaging nuclear-specific fluorescence in the excised surgical specimen and on extracting nuclear morphometric parameters (size, number, and area fraction) from the spatial distribution of the observed fluorescence in the tissue. We also report the utility of tissue topology in tumor margin assessment by measuring the fractal dimension in the same set of images. By a systematic analysis of multiple breast tissues specimens, we show here that the proposed method is not only accurate (~97% sensitivity and 96% specificity) in thin sections, but also in three-dimensional (3D) thick tissues that mimic the realistic lumpectomy specimens. Our data clearly precludes the utility of nuclear size as a reliable diagnostic criterion for tumor margin assessment. On the other hand, nuclear area fraction addresses this issue very

  16. Putatively novel serotypes and the potential for reduced vaccine effectiveness: capsular locus diversity revealed among 5405 pneumococcal genomes

    PubMed Central

    van Tonder, Andries J.; Bray, James E.; Quirk, Sigríður J.; Haraldsson, Gunnsteinn; Jolley, Keith A.; Maiden, Martin C. J.; Hoffmann, Steen; Bentley, Stephen D.; Haraldsson, Ásgeir; Erlendsdóttir, Helga; Kristinsson, Karl G.; Brueggemann, Angela B.

    2017-01-01

    The pneumococcus is a leading global pathogen and a key virulence factor possessed by the majority of pneumococci is an antigenic polysaccharide capsule (‘serotype’), which is encoded by the capsular (cps) locus. Approximately 100 different serotypes are known, but the extent of sequence diversity within the cps loci of individual serotypes is not well understood. Investigating serotype-specific sequence variation is crucial to the design of sequence-based serotyping methodology, understanding pneumococcal conjugate vaccine (PCV) effectiveness and the design of future PCVs. The availability of large genome datasets makes it possible to assess population-level variation among pneumococcal serotypes and in this study 5405 pneumococcal genomes were used to investigate cps locus diversity among 49 different serotypes. Pneumococci had been recovered between 1916 and 2014 from people of all ages living in 51 countries. Serotypes were deduced bioinformatically, cps locus sequences were extracted and variation was assessed within the cps locus, in the context of pneumococcal genetic lineages. Overall, cps locus sequence diversity varied markedly: low to moderate diversity was revealed among serogroups/types 1, 3, 7, 9, 11 and 22; whereas serogroups/types 6, 19, 23, 14, 15, 18, 33 and 35 displayed high diversity. Putative novel and/or hybrid cps loci were identified among all serogroups/types apart from 1, 3 and 9. This study demonstrated that cps locus sequence diversity varied widely between serogroups/types. Investigation of the biochemical structure of the polysaccharide capsule of major variants, particularly PCV-related serotypes and those that appear to be novel or hybrids, is warranted. PMID:28133541

  17. Absolute pitch: evidence for early cognitive facilitation during passive listening as revealed by reduced P3a amplitudes.

    PubMed

    Rogenmoser, Lars; Elmer, Stefan; Jäncke, Lutz

    2015-03-01

    Absolute pitch (AP) is the rare ability to identify or produce different pitches without using reference tones. At least two sequential processing stages are assumed to contribute to this phenomenon. The first recruits a pitch memory mechanism at an early stage of auditory processing, whereas the second is driven by a later cognitive mechanism (pitch labeling). Several investigations have used active tasks, but it is unclear how these two mechanisms contribute to AP during passive listening. The present work investigated the temporal dynamics of tone processing in AP and non-AP (NAP) participants by using EEG. We applied a passive oddball paradigm with between- and within-tone category manipulations and analyzed the MMN reflecting the early stage of auditory processing and the P3a response reflecting the later cognitive mechanism during the second processing stage. Results did not reveal between-group differences in MMN waveforms. By contrast, the P3a response was specifically associated with AP and sensitive to the processing of different pitch types. Specifically, AP participants exhibited smaller P3a amplitudes, especially in between-tone category conditions, and P3a responses correlated significantly with the age of commencement of musical training, suggesting an influence of early musical exposure on AP. Our results reinforce the current opinion that the representation of pitches at the processing level of the auditory-related cortex is comparable among AP and NAP participants, whereas the later processing stage is critical for AP. Results are interpreted as reflecting cognitive facilitation in AP participants, possibly driven by the availability of multiple codes for tones.

  18. Voxel-based morphometry in autopsy proven PSP and CBD.

    PubMed

    Josephs, Keith A; Whitwell, Jennifer L; Dickson, Dennis W; Boeve, Bradley F; Knopman, David S; Petersen, Ronald C; Parisi, Joseph E; Jack, Clifford R

    2008-02-01

    The aim of this study was to compare the patterns of grey and white matter atrophy on MRI in autopsy confirmed progressive supranuclear palsy (PSP) and corticobasal degeneration (CBD), and to determine whether the patterns vary depending on the clinical syndrome. Voxel-based morphometry was used to compare patterns of atrophy in 13 PSP and 11 CBD subjects and 24 controls. PSP and CBD subjects were also subdivided into those with a dominant dementia or extrapyramidal syndrome. PSP subjects showed brainstem atrophy with involvement of the cortex and underlying white matter. Frontoparietal grey and subcortical grey matter atrophy occurred in CBD. When subdivided, PSP subjects with an extrapyramidal syndrome had more brainstem atrophy and less cortical atrophy than CBD subjects with an extrapyramidal syndrome. PSP subjects with a dementia syndrome had more subcortical white matter atrophy than CBD subjects with a dementia syndrome. These results show regional differences between PSP and CBD that are useful in predicting the underlying pathology, and help to shed light on the in vivo distribution of regional atrophy in PSP and CBD.

  19. Voxel Based Morphometry in Optical Coherence Tomography: Validation & Core Findings

    PubMed Central

    Antony, Bhavna J.; Chen, Min; Carass, Aaron; Jedynak, Bruno M.; Al-Louzi, Omar; Solomon, Sharon D.; Saidha, Shiv; Calabresi, Peter A.; Prince, Jerry L.

    2016-01-01

    Optical coherence tomography (OCT) of the human retina is now becoming established as an important modality for the detection and tracking of various ocular diseases. Voxel based morphometry (VBM) is a long standing neuroimaging analysis technique that allows for the exploration of the regional differences in the brain. There has been limited work done in developing registration based methods for OCT, which has hampered the advancement of VBM analyses in OCT based population studies. Following on from our recent development of an OCT registration method, we explore the potential benefits of VBM analysis in cohorts of healthy controls (HCs) and multiple sclerosis (MS) patients. Specifically, we validate the stability of VBM analysis in two pools of HCs showing no significant difference between the two populations. Additionally, we also present a retrospective study of age and sex matched HCs and relapsing remitting MS patients, demonstrating results consistent with the reported literature while providing insight into the retinal changes associated with this MS subtype. PMID:27199503

  20. Shape Classification Using Wasserstein Distance for Brain Morphometry Analysis.

    PubMed

    Su, Zhengyu; Zeng, Wei; Wang, Yalin; Lu, Zhong-Lin; Gu, Xianfeng

    2015-01-01

    Brain morphometry study plays a fundamental role in medical imaging analysis and diagnosis. This work proposes a novel framework for brain cortical surface classification using Wasserstein distance, based on uniformization theory and Riemannian optimal mass transport theory. By Poincare uniformization theorem, all shapes can be conformally deformed to one of the three canonical spaces: the unit sphere, the Euclidean plane or the hyperbolic plane. The uniformization map will distort the surface area elements. The area-distortion factor gives a probability measure on the canonical uniformization space. All the probability measures on a Riemannian manifold form the Wasserstein space. Given any 2 probability measures, there is a unique optimal mass transport map between them, the transportation cost defines the Wasserstein distance between them. Wasserstein distance gives a Riemannian metric for the Wasserstein space. It intrinsically measures the dissimilarities between shapes and thus has the potential for shape classification. To the best of our knowledge, this is the first. work to introduce the optimal mass transport map to general Riemannian manifolds. The method is based on geodesic power Voronoi diagram. Comparing to the conventional methods, our approach solely depends on Riemannian metrics and is invariant under rigid motions and scalings, thus it intrinsically measures shape distance. Experimental results on classifying brain cortical surfaces with different intelligence quotients demonstrated the efficiency and efficacy of our method.

  1. Stereological Cell Morphometry In Right Atrium Myocardium Of Primates

    NASA Astrophysics Data System (ADS)

    Mandarim-De-Lacerda, Carlos A...; Hureau, Jacques

    1986-07-01

    The mechanism by which the cardiac impulse is propagated in normal hearts from its origin in the sinus node to the atrio-ventricular node has not been agreed on fully. We studied the "internodal posterior tract" through the crista terminalis by light microscopy and stereological morphometry. The hearts of 12 Papio cynocephalus were perfused , after sacrifice,with phosphate-buffered formol saline. The regions of the crista terminalis (CT), interatrial septum (IAS), atrioventricular bundle (AVB) and interventricular septum (IVS) were cut off and embedded in paraplast and sectioned (10 4m). The multipurpose test system M 42 was superimposed over the photomicrographs (1,890 points test, ESR = 2%) to the stereological computing. The quantitative results show that the cells from CT were more closely relationed with IAS cells than others cells (IVS and AVB cells). This results are not a morphological evidence to establish the specificity of the "internodal posterior tract". The cellular arrangement and anatomical variation in CT myocardium is very important.

  2. Shape Classification Using Wasserstein Distance for Brain Morphometry Analysis

    PubMed Central

    Su, Zhengyu; Zeng, Wei; Wang, Yalin; Lu, Zhong-Lin; Gu, Xianfeng

    2015-01-01

    Brain morphometry study plays a fundamental role in medical imaging analysis and diagnosis. This work proposes a novel framework for brain cortical surface classification using Wasserstein distance, based on uniformization theory and Riemannian optimal mass transport theory. By Poincare uniformization theorem, all shapes can be conformally deformed to one of the three canonical spaces: the unit sphere, the Euclidean plane or the hyperbolic plane. The uniformization map will distort the surface area elements. The area-distortion factor gives a probability measure on the canonical uniformization space. All the probability measures on a Riemannian manifold form the Wasserstein space. Given any 2 probability measures, there is a unique optimal mass transport map between them, the transportation cost defines the Wasserstein distance between them. Wasserstein distance gives a Riemannian metric for the Wasserstein space. It intrinsically measures the dissimilarities between shapes and thus has the potential for shape classification. To the best of our knowledge, this is the first work to introduce the optimal mass transport map to general Riemannian manifolds. The method is based on geodesic power Voronoi diagram. Comparing to the conventional methods, our approach solely depends on Riemannian metrics and is invariant under rigid motions and scalings, thus it intrinsically measures shape distance. Experimental results on classifying brain cortical surfaces with different intelligence quotients demonstrated the efficiency and efficacy of our method. PMID:26221691

  3. Responses of two semiarid conifer tree species to reduced precipitation and warming reveal new perspectives for stomatal regulation

    DOE PAGES

    Garcia-Forner, Nuria; Adams, Henry D.; Sevanto, Sanna; ...

    2015-08-08

    Here, relatively anisohydric species are predicted to be more predisposed to hydraulic failure than relatively isohydric species, as they operate with narrower hydraulic safety margins. We subjected co-occurring anisohydric Juniperus monosperma and isohydric Pinus edulis trees to warming, reduced precipitation, or both, and measured their gas exchange and hydraulic responses. We found that reductions in stomatal conductance and assimilation by heat and drought were more frequent during relatively moist periods, but these effects were not exacerbated in the combined heat and drought treatment. Counter to expectations, both species exhibited similar gs temporal dynamics in response to drought. Further, whereas P.more » edulis exhibited chronic embolism, J. monosperma showed very little embolism due to its conservative stomatal regulation and maintenance of xylem water potential above the embolism entry point. This tight stomatal control and low levels of embolism experienced by juniper refuted the notion that very low water potentials during drought are associated with loose stomatal control and with the hypothesis that anisohydric species are more prone to hydraulic failure than isohydric species. Because direct association of stomatal behaviour with embolism resistance can be misleading, we advocate consideration of stomatal behaviour relative to embolism resistance for classifying species drought response strategies.« less

  4. Real-time imaging of cotranscriptional splicing reveals a kinetic model that reduces noise: implications for alternative splicing regulation

    PubMed Central

    Schmidt, Ute; Robert, Marie-Cécile; Yoshida, Minoru; Villemin, Jean-Philippe; Auboeuf, Didier; Aitken, Stuart

    2011-01-01

    Splicing is a key process that expands the coding capacity of genomes. Its kinetics remain poorly characterized, and the distribution of splicing time caused by the stochasticity of single splicing events is expected to affect regulation efficiency. We conducted a small-scale survey on 40 introns in human cells and observed that most were spliced cotranscriptionally. Consequently, we constructed a reporter system that splices cotranscriptionally and can be monitored in live cells and in real time through the use of MS2–GFP. All small nuclear ribonucleoproteins (snRNPs) are loaded on nascent pre-mRNAs, and spliceostatin A inhibits splicing but not snRNP recruitment. Intron removal occurs in minutes and is best described by a model where several successive steps are rate limiting. Each pre-mRNA molecule is predicted to require a similar time to splice, reducing kinetic noise and improving the regulation of alternative splicing. This model is relevant to other kinetically controlled processes acting on few molecules. PMID:21624952

  5. Reduced Mismatch Repair of Heteroduplexes Reveals “Non”-interfering Crossing Over in Wild-Type Saccharomyces cerevisiae

    PubMed Central

    Getz, Tony J.; Banse, Stephen A.; Young, Lisa S.; Banse, Allison V.; Swanson, Johanna; Wang, Grace M.; Browne, Barclay L.; Foss, Henriette M.; Stahl, Franklin W.

    2008-01-01

    Using small palindromes to monitor meiotic double-strand-break-repair (DSBr) events, we demonstrate that two distinct classes of crossovers occur during meiosis in wild-type yeast. We found that crossovers accompanying 5:3 segregation of a palindrome show no conventional (i.e., positive) interference, while crossovers with 6:2 or normal 4:4 segregation for the same palindrome, in the same cross, do manifest interference. Our observations support the concept of a “non”-interference class and an interference class of meiotic double-strand-break-repair events, each with its own rules for mismatch repair of heteroduplexes. We further show that deletion of MSH4 reduces crossover tetrads with 6:2 or normal 4:4 segregation more than it does those with 5:3 segregation, consistent with Msh4p specifically promoting formation of crossovers in the interference class. Additionally, we present evidence that an ndj1 mutation causes a shift of noncrossovers to crossovers specifically within the “non”-interference class of DSBr events. We use these and other data in support of a model in which meiotic recombination occurs in two phases—one specializing in homolog pairing, the other in disjunction—and each producing both noncrossovers and crossovers. PMID:18385111

  6. Metatranscriptome of an Anaerobic Benzene-Degrading, Nitrate-Reducing Enrichment Culture Reveals Involvement of Carboxylation in Benzene Ring Activation

    PubMed Central

    Luo, Fei; Gitiafroz, Roya; Devine, Cheryl E.; Gong, Yunchen; Hug, Laura A.; Raskin, Lutgarde

    2014-01-01

    The enzymes involved in the initial steps of anaerobic benzene catabolism are not known. To try to elucidate this critical step, a metatranscriptomic analysis was conducted to compare the genes transcribed during the metabolism of benzene and benzoate by an anaerobic benzene-degrading, nitrate-reducing enrichment culture. RNA was extracted from the mixed culture and sequenced without prior mRNA enrichment, allowing simultaneous examination of the active community composition and the differential gene expression between the two treatments. Ribosomal and mRNA sequences attributed to a member of the family Peptococcaceae from the order Clostridiales were essentially only detected in the benzene-amended culture samples, implicating this group in the initial catabolism of benzene. Genes similar to each of two subunits of a proposed benzene-carboxylating enzyme were transcribed when the culture was amended with benzene. Anaerobic benzoate degradation genes from strict anaerobes were transcribed only when the culture was amended with benzene. Genes for other benzoate catabolic enzymes and for nitrate respiration were transcribed in both samples, with those attributed to an Azoarcus species being most abundant. These findings indicate that the mineralization of benzene starts with its activation by a strict anaerobe belonging to the Peptococcaceae, involving a carboxylation step to form benzoate. These data confirm the previously hypothesized syntrophic association between a benzene-degrading Peptococcaceae strain and a benzoate-degrading denitrifying Azoarcus strain for the complete catabolism of benzene with nitrate as the terminal electron acceptor. PMID:24795366

  7. Responses of two semiarid conifer tree species to reduced precipitation and warming reveal new perspectives for stomatal regulation

    SciTech Connect

    Garcia-Forner, Nuria; Adams, Henry D.; Sevanto, Sanna; Collins, Adam D.; Dickman, Lee T.; Hudson, Patrick J.; Zeppel, Melanie J. B.; Jenkins, Michael W.; Powers, Heath; Martinez-Vilalta, Jordi; Mcdowell, Nate G.

    2015-08-08

    Here, relatively anisohydric species are predicted to be more predisposed to hydraulic failure than relatively isohydric species, as they operate with narrower hydraulic safety margins. We subjected co-occurring anisohydric Juniperus monosperma and isohydric Pinus edulis trees to warming, reduced precipitation, or both, and measured their gas exchange and hydraulic responses. We found that reductions in stomatal conductance and assimilation by heat and drought were more frequent during relatively moist periods, but these effects were not exacerbated in the combined heat and drought treatment. Counter to expectations, both species exhibited similar gs temporal dynamics in response to drought. Further, whereas P. edulis exhibited chronic embolism, J. monosperma showed very little embolism due to its conservative stomatal regulation and maintenance of xylem water potential above the embolism entry point. This tight stomatal control and low levels of embolism experienced by juniper refuted the notion that very low water potentials during drought are associated with loose stomatal control and with the hypothesis that anisohydric species are more prone to hydraulic failure than isohydric species. Because direct association of stomatal behaviour with embolism resistance can be misleading, we advocate consideration of stomatal behaviour relative to embolism resistance for classifying species drought response strategies.

  8. Reduced chondrogenic matrix accumulation by 4-methylumbelliferone reveals the potential for selective targeting of UDP-glucose dehydrogenase.

    PubMed

    Clarkin, C E; Allen, S; Wheeler-Jones, C P; Bastow, E R; Pitsillides, A A

    2011-04-01

    4-Methylumbelliferone (4-MU) is described as a selective inhibitor of hyaluronan (HA) production. It is thought that 4-MU depletes UDP-glucuronic acid (UDP-GlcUA) substrate for HA synthesis and also suppresses HA-synthase expression. The possibility that 4-MU exerts at least some of its actions via regulation of UDP-glucose dehydrogenase (UGDH), a key enzyme required for both HA and sulphated-glycosaminoglycan (sGAG) production, remains unexplored. We therefore examined the effects of 4-MU on basal and retroviral UGDH-driven HA and sGAG release in cells derived from chick articular cartilage and its influence upon UGDH protein and mRNA expression and HA and sGAG production. We found that 4-MU: i) suppressed UGDH mRNA and protein expression and chondrogenic matrix accumulation in chick limb bud micromass culture, ii) significantly reduced both HA and sGAG production and iii) more selectively reversed the potentiating effects of UGDH overexpression on the production of HA than sGAG. Understanding how GAG synthesis is controlled and the mechanism of 4-MU action may inform its future clinical success.

  9. Reduced chondrogenic matrix accumulation by 4-methylumbelliferone reveals the potential for selective targeting of UDP-glucose dehydrogenase

    PubMed Central

    Clarkin, C.E.; Allen, S.; Wheeler-Jones, C.P.; Bastow, E.R.; Pitsillides, A.A.

    2011-01-01

    4-Methylumbelliferone (4-MU) is described as a selective inhibitor of hyaluronan (HA) production. It is thought that 4-MU depletes UDP-glucuronic acid (UDP-GlcUA) substrate for HA synthesis and also suppresses HA-synthase expression. The possibility that 4-MU exerts at least some of its actions via regulation of UDP-glucose dehydrogenase (UGDH), a key enzyme required for both HA and sulphated-glycosaminoglycan (sGAG) production, remains unexplored. We therefore examined the effects of 4-MU on basal and retroviral UGDH-driven HA and sGAG release in cells derived from chick articular cartilage and its influence upon UGDH protein and mRNA expression and HA and sGAG production. We found that 4-MU: i) suppressed UGDH mRNA and protein expression and chondrogenic matrix accumulation in chick limb bud micromass culture, ii) significantly reduced both HA and sGAG production and iii) more selectively reversed the potentiating effects of UGDH overexpression on the production of HA than sGAG. Understanding how GAG synthesis is controlled and the mechanism of 4-MU action may inform its future clinical success. PMID:21292001

  10. Deep sequencing analysis reveals a TMV mutant with a poly(A) tract reduces host defense responses in Nicotiana benthamiana.

    PubMed

    Guo, Song; Wong, Sek-Man

    2017-07-15

    Tobacco mosaic virus (TMV) possesses an upstream pseudoknotted domain (UPD), which is important for replication. After substituting the UPD with an internal poly(A) tract (43 nt), a mutant TMV-43A was constructed. TMV-43A replicated slower than TMV and induced a non-lethal mosaic symptom in Nicotiana benthamiana. In this study, deep sequencing was performed to detect the differences of small RNA profiles between TMV- and TMV-43A-infected N. benthamiana. The results showed that TMV-43A produced lesser amount of virus-derived interfering RNAs (vsiRNAs) than that of TMV. However, the distributions of vsiRNAs generation hotspots between TMV and TMV-43A were similar. Expression of genes related to small RNA biogenesis in TMV-43A-infected N. benthamiana was significantly lower than that of TMV, which leads to generation of lesser vsiRNAs. The expressions of host defense response genes were up-regulated after TMV infection, as compared to TMV-43A-infected plants. Host defense response to TMV-43A infection was lower than that to TMV. The absence of UPD might contribute to the reduced host response to TMV-43A. Our study provides valuable information in the role of the UPD in eliciting host response genes after TMV infection in N. benthamiana. (187 words). Copyright © 2017 Elsevier B.V. All rights reserved.

  11. Responses of two semiarid conifer tree species to reduced precipitation and warming reveal new perspectives for stomatal regulation.

    PubMed

    Garcia-Forner, Núria; Adams, Henry D; Sevanto, Sanna; Collins, Adam D; Dickman, Lee T; Hudson, Patrick J; Zeppel, Melanie J B; Jenkins, Michael W; Powers, Heath; Martínez-Vilalta, Jordi; Mcdowell, Nate G

    2016-01-01

    Relatively anisohydric species are predicted to be more predisposed to hydraulic failure than relatively isohydric species, as they operate with narrower hydraulic safety margins. We subjected co-occurring anisohydric Juniperus monosperma and isohydric Pinus edulis trees to warming, reduced precipitation, or both, and measured their gas exchange and hydraulic responses. We found that reductions in stomatal conductance and assimilation by heat and drought were more frequent during relatively moist periods, but these effects were not exacerbated in the combined heat and drought treatment. Counter to expectations, both species exhibited similar gs temporal dynamics in response to drought. Further, whereas P. edulis exhibited chronic embolism, J. monosperma showed very little embolism due to its conservative stomatal regulation and maintenance of xylem water potential above the embolism entry point. This tight stomatal control and low levels of embolism experienced by juniper refuted the notion that very low water potentials during drought are associated with loose stomatal control and with the hypothesis that anisohydric species are more prone to hydraulic failure than isohydric species. Because direct association of stomatal behaviour with embolism resistance can be misleading, we advocate consideration of stomatal behaviour relative to embolism resistance for classifying species drought response strategies.

  12. Genomic and Proteomic Profiling Reveals Reduced Mitochondrial Function and Disruption of the Neuromuscular Junction Driving Rat Sarcopenia

    PubMed Central

    Ibebunjo, Chikwendu; Chick, Joel M.; Kendall, Tracee; Eash, John K.; Li, Christine; Zhang, Yunyu; Vickers, Chad; Wu, Zhidan; Clarke, Brian A.; Shi, Jun; Cruz, Joseph; Fournier, Brigitte; Brachat, Sophie; Gutzwiller, Sabine; Ma, QiCheng; Markovits, Judit; Broome, Michelle; Steinkrauss, Michelle; Skuba, Elizabeth; Galarneau, Jean-Rene; Gygi, Steven P.

    2013-01-01

    Molecular mechanisms underlying sarcopenia, the age-related loss of skeletal muscle mass and function, remain unclear. To identify molecular changes that correlated best with sarcopenia and might contribute to its pathogenesis, we determined global gene expression profiles in muscles of rats aged 6, 12, 18, 21, 24, and 27 months. These rats exhibit sarcopenia beginning at 21 months. Correlation of the gene expression versus muscle mass or age changes, and functional annotation analysis identified gene signatures of sarcopenia distinct from gene signatures of aging. Specifically, mitochondrial energy metabolism (e.g., tricarboxylic acid cycle and oxidative phosphorylation) pathway genes were the most downregulated and most significantly correlated with sarcopenia. Also, perturbed were genes/pathways associated with neuromuscular junction patency (providing molecular evidence of sarcopenia-related functional denervation and neuromuscular junction remodeling), protein degradation, and inflammation. Proteomic analysis of samples at 6, 18, and 27 months confirmed the depletion of mitochondrial energy metabolism proteins and neuromuscular junction proteins. Together, these findings suggest that therapeutic approaches that simultaneously stimulate mitochondrogenesis and reduce muscle proteolysis and inflammation have potential for treating sarcopenia. PMID:23109432

  13. Brain morphometry reproducibility in multi-center 3T MRI studies: a comparison of cross-sectional and longitudinal segmentations.

    PubMed

    Jovicich, Jorge; Marizzoni, Moira; Sala-Llonch, Roser; Bosch, Beatriz; Bartrés-Faz, David; Arnold, Jennifer; Benninghoff, Jens; Wiltfang, Jens; Roccatagliata, Luca; Nobili, Flavio; Hensch, Tilman; Tränkner, Anja; Schönknecht, Peter; Leroy, Melanie; Lopes, Renaud; Bordet, Régis; Chanoine, Valérie; Ranjeva, Jean-Philippe; Didic, Mira; Gros-Dagnac, Hélène; Payoux, Pierre; Zoccatelli, Giada; Alessandrini, Franco; Beltramello, Alberto; Bargalló, Núria; Blin, Olivier; Frisoni, Giovanni B

    2013-12-01

    Large-scale longitudinal multi-site MRI brain morphometry studies are becoming increasingly crucial to characterize both normal and clinical population groups using fully automated segmentation tools. The test-retest reproducibility of morphometry data acquired across multiple scanning sessions, and for different MR vendors, is an important reliability indicator since it defines the sensitivity of a protocol to detect longitudinal effects in a consortium. There is very limited knowledge about how across-session reliability of morphometry estimates might be affected by different 3T MRI systems. Moreover, there is a need for optimal acquisition and analysis protocols in order to reduce sample sizes. A recent study has shown that the longitudinal FreeSurfer segmentation offers improved within session test-retest reproducibility relative to the cross-sectional segmentation at one 3T site using a nonstandard multi-echo MPRAGE sequence. In this study we implement a multi-site 3T MRI morphometry protocol based on vendor provided T1 structural sequences from different vendors (3D MPRAGE on Siemens and Philips, 3D IR-SPGR on GE) implemented in 8 sites located in 4 European countries. The protocols used mild acceleration factors (1.5-2) when possible. We acquired across-session test-retest structural data of a group of healthy elderly subjects (5 subjects per site) and compared the across-session reproducibility of two full-brain automated segmentation methods based on either longitudinal or cross-sectional FreeSurfer processing. The segmentations include cortical thickness, intracranial, ventricle and subcortical volumes. Reproducibility is evaluated as absolute changes relative to the mean (%), Dice coefficient for volume overlap and intraclass correlation coefficients across two sessions. We found that this acquisition and analysis protocol gives comparable reproducibility results to previous studies that used longer acquisitions without acceleration. We also show that

  14. Strain-resolved Metatranscriptomic Analysis Reveals Unexpectedly Diverse Heterotrophic and Lithoautotrophic Microbial Metabolism in Naturally Reduced Aquifer Sediments

    NASA Astrophysics Data System (ADS)

    Beller, H. R.; Jewell, T. N. M.; Karaoz, U.; Bill, M.; Chakraborty, R.; Brodie, E.; Williams, K. H.

    2016-12-01

    In this study, we sought to better understand how natural organic matter fuels microbial communities in the anoxic subsurface at the Rifle (CO) site. We conducted a 20-day microcosm experiment with naturally reduced zone (NRZ) sediments and collected samples every 5 days for omics (metagenome and metatranscriptome) and geochemical measurements. No electron donors were added other than the NRZ sediment, which is enriched in buried woody plant material. The microcosms were constructed and incubated under anaerobic conditions in serum bottles with a N2 headspace. Biogeochemical measurements indicated that the decomposition of native organic matter occurred in different phases, including mineralization of dissolved organic carbon (DOC) to CO2 during the first week of incubation, followed by a pulse of acetogenesis that dominated carbon flux after 2 weeks. The depletion of DOC over time was strongly correlated with increases in expression of many genes associated with heterotrophy (e.g., amino acid, fatty acid, and carbohydrate metabolism) belonging to a Hydrogenophaga strain that accounted for a relatively large percentage ( 8%) of the metatranscriptome. This Hydrogenophaga strain also expressed genes indicative of chemolithoautotrophy, including CO2 fixation (RubisCO), H2 oxidation, S-compound oxidation, and denitrification. The pulse of acetogenesis appears to have been collectively catalyzed by a number of different organisms and metabolisms, most prominently pyruvate:ferredoxin oxidoreductase. Unexpected genes were identified among the most highly expressed (>98th percentile) transcripts, including acetone carboxylase and cell wall-associated hydrolases, some of which are known to act on peptidoglycan. Many of the most highly expressed hydrolases belonged to a Ca. Bathyarchaeota strain and may have been associated with scavenging of bacterial biomass. Overall, observed metabolism ranged far beyond the expected fermentation of plant-derived organic matter.

  15. Multivoxel pattern analysis reveals increased memory targeting and reduced use of retrieved details during single-agenda source monitoring.

    PubMed

    McDuff, Susan G R; Frankel, Hillary C; Norman, Kenneth A

    2009-01-14

    We used multivoxel pattern analysis (MVPA) of functional MRI (fMRI) data to gain insight into how subjects' retrieval agendas influence source memory judgments (was item X studied using source Y?). In Experiment 1, we used a single-agenda test where subjects judged whether items were studied with the targeted source or not. In Experiment 2, we used a multiagenda test where subjects judged whether items were studied using the targeted source, studied using a different source, or nonstudied. To evaluate the differences between single- and multiagenda source monitoring, we trained a classifier to detect source-specific fMRI activity at study, and then we applied the classifier to data from the test phase. We focused on trials where the targeted source and the actual source differed, so we could use MVPA to track neural activity associated with both the targeted source and the actual source. Our results indicate that single-agenda monitoring was associated with increased focus on the targeted source (as evidenced by increased targeted-source activity, relative to baseline) and reduced use of information relating to the actual, nontarget source. In the multiagenda experiment, high levels of actual-source activity were associated with increased correct rejections, suggesting that subjects were using recollection of actual-source information to avoid source memory errors. In the single-agenda experiment, there were comparable levels of actual-source activity (suggesting that recollection was taking place), but the relationship between actual-source activity and behavior was absent (suggesting that subjects were failing to make proper use of this information).

  16. Morphometry of the pituitary gland and hypothalamus in long-term survivors of childhood trauma.

    PubMed

    Porto, L; Margerkurth, J; Althaus, J; You, S-J; Zanella, F E; Kieslich, M

    2011-11-01

    Chronic pituitary dysfunction is increasingly recognized as a sequela of traumatic brain injury (TBI). Our aim was to rule out any late morphometric changes of the pituitary gland and hypothalamus in survivors of TBI during childhood requiring intensive care. We assessed morphometric abnormalities of the sella region and hypothalamus in patients who sustained TBI during childhood. The patients showed no clinical hormonal dysfunction at the acute phase and pituitary hormone levels at the time of our study were within normal limits. From the 18 enrolled patients in the magnetic resonance study, five were removed due to morphological changes or anatomical variations. We studied the MRI of 13 male survivors (mean age 27 years, mean time after trauma 20 years) and compared them to 13 male control subjects who were matched in terms of age (mean age, 26 years), education and ethnicity. Analyses of the pituitary gland and sella on a midsagittal T2- and T1-weighted image were performed. We used voxel-based morphometry (VBM), an unbiased MRI morphometric method to investigate hypothalamic region in this group of patients. There was only a trend towards a reduced pituitary gland width in the patient group compared to controls. However, no significant morphological and morphometric abnormality was seen and VBM showed no hypothalamic grey matter loss. In the absence of hormonal dysfunction, no persisting morphometric changes of the pituitary gland and hypothalamus were seen in survivors of childhood TBI requiring intensive care.

  17. Lung morphometry changes in prevention of airway remodeling by protocatechuic aldehyde in asthmatic mice

    PubMed Central

    Zhang, Jiankai; Ma, Mulan; Qin, Dongyun; Huang, Jianping; Cui, Xiaojun; Wu, Yongfu; Yang, Huiling; Fu, Hui; Liao, Cui

    2015-01-01

    Airway remodeling can lead to irreversible airflow obstruction and persistent airway hyper-responsiveness, which is the pathological basis of refractory asthma. To investigate the preventive effect of protocatechuic aldehyde on airway remodeling in asthmatic mice by lung morphometry methods. BALB/c mice were used to establish model of airway remodeling by ovalbumin (OVA) inhalation. Bronchoalveolar lavage fluid (BALF) were collected for eosinophils (EOS) count and detection of interleukin 4 (IL-4), interleukin-13 (IL-13) and interferon (IFN-γ) content. The left lung pathological sections were performed HE, AB-PAS and Masson staining. The epithelial lamina thickness of the left main bronchus (Re), the smooth muscle layer thickness (Rm), the number of goblet cells and goblet cell area percentage (%Ac) and gas side of the road and vascular collagen deposition (%Aco, %Avc) situation were measured. Protocatechuic aldehyde gavage made the reduction of BALF EOS count. IL-4 and IL-13 levels also decreased, while the IFN-γ level increased. The left main bronchus Re, Rm, goblet cell count, Ac% and Aco% and Avc% reduced. Protocatechuic aldehyde can significantly control airway inflammation and prevent airway remodeling. PMID:26221226

  18. Regional gray matter abnormalities in patients with schizophrenia determined with optimized voxel-based morphometry

    NASA Astrophysics Data System (ADS)

    Guo, XiaoJuan; Yao, Li; Jin, Zhen; Chen, Kewei

    2006-03-01

    This study examined regional gray matter abnormalities across the whole brain in 19 patients with schizophrenia (12 males and 7 females), comparing with 11 normal volunteers (7 males and 4 females). The customized brain templates were created in order to improve spatial normalization and segmentation. Then automated preprocessing of magnetic resonance imaging (MRI) data was conducted using optimized voxel-based morphometry (VBM). The statistical voxel based analysis was implemented in terms of two-sample t-test model. Compared with normal controls, regional gray matter concentration in patients with schizophrenia was significantly reduced in the bilateral superior temporal gyrus, bilateral middle frontal and inferior frontal gyrus, right insula, precentral and parahippocampal areas, left thalamus and hypothalamus as well as, however, significant increases in gray matter concentration were not observed across the whole brain in the patients. This study confirms and extends some earlier findings on gray matter abnormalities in schizophrenic patients. Previous behavior and fMRI researches on schizophrenia have suggested that cognitive capacity decreased and self-conscious weakened in schizophrenic patients. These regional gray matter abnormalities determined through structural MRI with optimized VBM may be potential anatomic underpinnings of schizophrenia.

  19. Morphometry, Bite-Force, and Paleobiology of the Late Miocene Caiman Purussaurus brasiliensis

    PubMed Central

    Aureliano, Tito; Ghilardi, Aline M.; Guilherme, Edson; Souza-Filho, Jonas P.; Cavalcanti, Mauro; Riff, Douglas

    2015-01-01

    Purussaurus brasiliensis thrived in the northwestern portion of South America during the Late Miocene. Although substantial material has been recovered since its early discovery, this fossil crocodilian can still be considered as very poorly understood. In the present work, we used regression equations based on modern crocodilians to present novel details about the morphometry, bite-force and paleobiology of this species. According to our results, an adult Purussaurus brasiliensis was estimated to reach around 12.5 m in length, weighing around 8.4 metric tons, with a mean daily food intake of 40.6 kg. It was capable of generating sustained bite forces of 69,000 N (around 7 metric tons-force). The extreme size and strength reached by this animal seems to have allowed it to include a wide range of prey in its diet, making it a top predator in its ecosystem. As an adult, it would have preyed upon large to very large vertebrates, and, being unmatched by any other carnivore, it avoided competition. The evolution of a large body size granted P. brasiliensis many advantages, but it may also have led to its vulnerability. The constantly changing environment on a large geological scale may have reduced its long-term survival, favoring smaller species more resilient to ecological shifts. PMID:25689140

  20. Comparison of Prostatic Tissue Processed by Microwave and Conventional Technique Using Morphometry

    PubMed Central

    Jain, Promil; Kumar, Sanjay; Arora, B; Singh, Sneh; Chabbra, Sonia; Sen, Rajeev

    2015-01-01

    Background and Objectives: Rapid processing of histopathological specimens and decreased turnaround time is important to fulfill the needs of clinicians treating sick patients, so the present study was conducted to compare the time taken and quality of sections in processing of prostatic tissue by rapid microwave and conventional techniques using morphometry. Methods: Four to five mm thick paired prostate tissue pieces of fifty cases of prostatectomy specimens were taken. One tissue piece of the pair was processed routinely overnight by conventional tissue processing and the other by microwave processing. Time taken for processing by both conventional technique and microwave technique was noted and compared. Then, both were stained with conventional method of hematoxylin and eosin staining and examined for histological typing and grading. Morphometric study was done on slides of prostatic tissue processed by both conventional and microwave technique. Result: The prostatectomy specimens included both benign (86%) and malignant (14%) prostatic lesions in the age range of 46-85 years. The time taken for steps of dehydration, clearing and impregnation in microwave technique was significantly less as compared to histoprocessing done by conventional technique. Morphology, staining patterns of prostatic tissue processed within minutes by microwave technique, whether benign or malignant, were comparable to those sections which were processed in days using standard technique. Conclusion: Domestic microwave oven can be used for histoprocessing to accelerate the processing with preservation of morphology and is cheaper than commercially available microwave ovens and processing time was considerably reduced from days to minutes. PMID:26516319

  1. Computational Morphometry for Detecting Changes in Brain Structure Due to Development, Aging, Learning, Disease and Evolution

    PubMed Central

    Mietchen, Daniel; Gaser, Christian

    2009-01-01

    The brain, like any living tissue, is constantly changing in response to genetic and environmental cues and their interaction, leading to changes in brain function and structure, many of which are now in reach of neuroimaging techniques. Computational morphometry on the basis of Magnetic Resonance (MR) images has become the method of choice for studying macroscopic changes of brain structure across time scales. Thanks to computational advances and sophisticated study designs, both the minimal extent of change necessary for detection and, consequently, the minimal periods over which such changes can be detected have been reduced considerably during the last few years. On the other hand, the growing availability of MR images of more and more diverse brain populations also allows more detailed inferences about brain changes that occur over larger time scales, way beyond the duration of an average research project. On this basis, a whole range of issues concerning the structures and functions of the brain are now becoming addressable, thereby providing ample challenges and opportunities for further contributions from neuroinformatics to our understanding of the brain and how it changes over a lifetime and in the course of evolution. PMID:19707517

  2. Comparison of Prostatic Tissue Processed by Microwave and Conventional Technique Using Morphometry.

    PubMed

    Jain, Promil; Kumar, Sanjay; Arora, B; Singh, Sneh; Chabbra, Sonia; Sen, Rajeev

    2015-01-01

    Rapid processing of histopathological specimens and decreased turnaround time is important to fulfill the needs of clinicians treating sick patients, so the present study was conducted to compare the time taken and quality of sections in processing of prostatic tissue by rapid microwave and conventional techniques using morphometry. Four to five mm thick paired prostate tissue pieces of fifty cases of prostatectomy specimens were taken. One tissue piece of the pair was processed routinely overnight by conventional tissue processing and the other by microwave processing. Time taken for processing by both conventional technique and microwave technique was noted and compared. Then, both were stained with conventional method of hematoxylin and eosin staining and examined for histological typing and grading. Morphometric study was done on slides of prostatic tissue processed by both conventional and microwave technique. The prostatectomy specimens included both benign (86%) and malignant (14%) prostatic lesions in the age range of 46-85 years. The time taken for steps of dehydration, clearing and impregnation in microwave technique was significantly less as compared to histoprocessing done by conventional technique. Morphology, staining patterns of prostatic tissue processed within minutes by microwave technique, whether benign or malignant, were comparable to those sections which were processed in days using standard technique. Domestic microwave oven can be used for histoprocessing to accelerate the processing with preservation of morphology and is cheaper than commercially available microwave ovens and processing time was considerably reduced from days to minutes.

  3. Progress in Using Brain Morphometry as a Clinical Tool for Diagnosing Psychiatric Disorders

    PubMed Central

    Haubold, Alexander; Peterson, Bradley S.; Bansal, Ravi

    2014-01-01

    Brain morphometry in recent decades has increased our understanding of the neural bases of psychiatric disorders by localizing anatomical disturbances to specific nuclei and subnuclei of the brain. At least some of these disturbances precede the overt expression of clinical symptoms and possibly are endophenotypes that could be used to diagnose an individual accurately as having a specific psychiatric disorder. More accurate diagnoses could significantly reduce the emotional and financial burden of disease by aiding clinicians in implementing appropriate treatments earlier and in tailoring treatment to the individual needs. Several methods, especially those based on machine learning, have been proposed that use anatomical brain measures and gold-standard diagnoses of participants to learn decision rules that classify a person automatically as having one disorder rather than another. We review the general principles and procedures for machine learning, particularly as applied to diagnostic classification, and then review the procedures that have thus far attempted to diagnose psychiatric illnesses automatically using anatomical measures of the brain. We discuss the strengths and limitations of extant procedures and note that the sensitivity and specificity of these procedures in their most successful implementations have approximated 90%. Although these methods have not yet been applied within clinical settings, they provide strong evidence that individual patients can be diagnosed accurately using the spatial pattern of disturbances across the brain. PMID:22394424

  4. The brain structure correlates of individual differences in trait mindfulness: a voxel-based morphometry study.

    PubMed

    Lu, H; Song, Y; Xu, M; Wang, X; Li, X; Liu, J

    2014-07-11

    Mindfulness is the state of being attentive to and aware of what is taking place in the present, which is beneficial for reducing stress-related symptoms and improving mental and physical health. Previous studies have demonstrated that meditation practice can improve individuals' mindfulness through modifying functions and structures of multiple brain regions, including the anterior cingulate cortex (ACC), insula, fronto-limbic network, posterior cingulate cortex (PCC), and temporal-parietal junction. However, little is known about the neuroanatomical correlates of trait mindfulness. In the current study, we used voxel-based morphometry to investigate the neural correlates of individual differences in trait mindfulness by correlating the gray matter (GM) volume of each voxel across the whole brain with trait mindfulness measured by the Mindful Attention Awareness Scale in a large sample of young adults (N=247). We found that individuals who were more mindful of the present had greater GM volume in the right hippocampus/amygdala and bilateral ACC, but less GM volume in bilateral PCC and the left orbitofrontal cortex. These results suggest that trait mindfulness is associated with brain regions involved in executive attention, emotion regulation, and self-referential processing, through which mindfulness may exert its beneficial effects on psychological and physical well-being.

  5. Brain structure in post-traumatic stress disorder: A voxel-based morphometry analysis

    PubMed Central

    Tan, Liwen; Zhang, Li; Qi, Rongfeng; Lu, Guangming; Li, Lingjiang; Liu, Jun; Li, Weihui

    2013-01-01

    This study compared the difference in brain structure in 12 mine disaster survivors with chronic post-traumatic stress disorder, 7 cases of improved post-traumatic stress disorder symptoms, and 14 controls who experienced the same mine disaster but did not suffer post-traumatic stress disorder, using the voxel-based morphometry method. The correlation between differences in brain structure and post-traumatic stress disorder symptoms was also investigated. Results showed that the gray matter volume was the highest in the trauma control group, followed by the symptoms-improved group, and the lowest in the chronic post-traumatic stress disorder group. Compared with the symptoms-improved group, the gray matter volume in the lingual gyrus of the right occipital lobe was reduced in the chronic post-traumatic stress disorder group. Compared with the trauma control group, the gray matter volume in the right middle occipital gyrus and left middle frontal gyrus was reduced in the symptoms-improved group. Compared with the trauma control group, the gray matter volume in the left superior parietal lobule and right superior frontal gyrus was reduced in the chronic post-traumatic stress disorder group. The gray matter volume in the left superior parietal lobule was significantly positively correlated with the State-Trait Anxiety Inventory subscale score in the symptoms-improved group and chronic post-traumatic stress disorder group (r = 0.477, P = 0.039). Our findings indicate that (1) chronic post-traumatic stress disorder patients have gray matter structural damage in the prefrontal lobe, occipital lobe, and parietal lobe, (2) after post-traumatic stress, the disorder symptoms are improved and gray matter structural damage is reduced, but cannot recover to the trauma-control level, and (3) the superior parietal lobule is possibly associated with chronic post-traumatic stress disorder. Post-traumatic stress disorder patients exhibit gray matter abnormalities. PMID:25206550

  6. Brain structure in post-traumatic stress disorder: A voxel-based morphometry analysis.

    PubMed

    Tan, Liwen; Zhang, Li; Qi, Rongfeng; Lu, Guangming; Li, Lingjiang; Liu, Jun; Li, Weihui

    2013-09-15

    This study compared the difference in brain structure in 12 mine disaster survivors with chronic post-traumatic stress disorder, 7 cases of improved post-traumatic stress disorder symptoms, and 14 controls who experienced the same mine disaster but did not suffer post-traumatic stress disorder, using the voxel-based morphometry method. The correlation between differences in brain structure and post-traumatic stress disorder symptoms was also investigated. Results showed that the gray matter volume was the highest in the trauma control group, followed by the symptoms-improved group, and the lowest in the chronic post-traumatic stress disorder group. Compared with the symptoms-improved group, the gray matter volume in the lingual gyrus of the right occipital lobe was reduced in the chronic post-traumatic stress disorder group. Compared with the trauma control group, the gray matter volume in the right middle occipital gyrus and left middle frontal gyrus was reduced in the symptoms-improved group. Compared with the trauma control group, the gray matter volume in the left superior parietal lobule and right superior frontal gyrus was reduced in the chronic post-traumatic stress disorder group. The gray matter volume in the left superior parietal lobule was significantly positively correlated with the State-Trait Anxiety Inventory subscale score in the symptoms-improved group and chronic post-traumatic stress disorder group (r = 0.477, P = 0.039). Our findings indicate that (1) chronic post-traumatic stress disorder patients have gray matter structural damage in the prefrontal lobe, occipital lobe, and parietal lobe, (2) after post-traumatic stress, the disorder symptoms are improved and gray matter structural damage is reduced, but cannot recover to the trauma-control level, and (3) the superior parietal lobule is possibly associated with chronic post-traumatic stress disorder. Post-traumatic stress disorder patients exhibit gray matter abnormalities.

  7. Larger right posterior parietal volume in action video game experts: a behavioral and voxel-based morphometry (VBM) study.

    PubMed

    Tanaka, Satoshi; Ikeda, Hanako; Kasahara, Kazumi; Kato, Ryo; Tsubomi, Hiroyuki; Sugawara, Sho K; Mori, Makoto; Hanakawa, Takashi; Sadato, Norihiro; Honda, Manabu; Watanabe, Katsumi

    2013-01-01

    Recent studies suggest that action video game players exhibit superior performance in visuospatial cognitive tasks compared with non-game players. However, the neural basis underlying this visuospatial cognitive performance advantage remains largely unknown. The present human behavioral and imaging study compared gray matter volume in action video game experts and non-experts using structural magnetic resonance imaging and voxel-based morphometry analysis. The results revealed significantly larger gray matter volume in the right posterior parietal cortex in experts compared with non-experts. Furthermore, the larger gray matter volume in the right posterior parietal cortex significantly correlated with individual performance in a visual working memory task in experts. These results suggest that differences in brain structure may be linked to extensive video game play, leading to superior visuospatial cognitive performance in action video game experts.

  8. Proteomics Analysis Revealed that Crosstalk between Helicobacter pylori and Streptococcus mitis May Enhance Bacterial Survival and Reduces Carcinogenesis.

    PubMed

    Khosravi, Yalda; Loke, Mun Fai; Goh, Khean Lee; Vadivelu, Jamuna

    2016-01-01

    Helicobacter pylori is the dominant species of the human gastric microbiota and is present in the stomach of more than half of the human population worldwide. Colonization by H. pylori causes persistent inflammatory response and H. pylori-induced gastritis is the strongest singular risk factor for the development of gastric adenocarcinoma. However, only a small proportion of infected individuals develop malignancy. Besides H. pylori, other microbial species have also been shown to be related to gastritis. We previously reported that interspecies microbial interaction between H. pylori and S. mitis resulted in alteration of their metabolite profiles. In this study, we followed up by analyzing the changing protein profiles of H. pylori and S. mitis by LC/Q-TOF mass spectrometry to understand the different response of the two bacterial species in a multi-species micro-environment. Differentially-expressed proteins in mono- and co-cultures could be mapped into 18 biological pathways. The number of proteins involve in RNA degradation, nucleotide excision repair, mismatch repair, and lipopolysaccharide (LPS) biosynthesis were increased in co-cultured H. pylori. On the other hand, fewer proteins involve in citrate cycle, glycolysis/ gluconeogenesis, aminoacyl-tRNA biosynthesis, translation, metabolism, and cell signaling were detected in co-cultured H. pylori. This is consistent with our previous observation that in the presence of S. mitis, H. pylori was transformed to coccoid. Interestingly, phosphoglycerate kinase (PGK), a major enzyme used in glycolysis, was found in abundance in co-cultured S. mitis and this may have enhanced the survival of S. mitis in the multi-species microenvironment. On the other hand, thioredoxin (TrxA) and other redox-regulating enzymes of H. pylori were less abundant in co-culture possibly suggesting reduced oxidative stress. Oxidative stress plays an important role in tissue damage and carcinogenesis. Using the in vitro co-culture model

  9. Proteomics Analysis Revealed that Crosstalk between Helicobacter pylori and Streptococcus mitis May Enhance Bacterial Survival and Reduces Carcinogenesis

    PubMed Central

    Khosravi, Yalda; Loke, Mun Fai; Goh, Khean Lee; Vadivelu, Jamuna

    2016-01-01

    Helicobacter pylori is the dominant species of the human gastric microbiota and is present in the stomach of more than half of the human population worldwide. Colonization by H. pylori causes persistent inflammatory response and H. pylori-induced gastritis is the strongest singular risk factor for the development of gastric adenocarcinoma. However, only a small proportion of infected individuals develop malignancy. Besides H. pylori, other microbial species have also been shown to be related to gastritis. We previously reported that interspecies microbial interaction between H. pylori and S. mitis resulted in alteration of their metabolite profiles. In this study, we followed up by analyzing the changing protein profiles of H. pylori and S. mitis by LC/Q-TOF mass spectrometry to understand the different response of the two bacterial species in a multi-species micro-environment. Differentially-expressed proteins in mono- and co-cultures could be mapped into 18 biological pathways. The number of proteins involve in RNA degradation, nucleotide excision repair, mismatch repair, and lipopolysaccharide (LPS) biosynthesis were increased in co-cultured H. pylori. On the other hand, fewer proteins involve in citrate cycle, glycolysis/ gluconeogenesis, aminoacyl-tRNA biosynthesis, translation, metabolism, and cell signaling were detected in co-cultured H. pylori. This is consistent with our previous observation that in the presence of S. mitis, H. pylori was transformed to coccoid. Interestingly, phosphoglycerate kinase (PGK), a major enzyme used in glycolysis, was found in abundance in co-cultured S. mitis and this may have enhanced the survival of S. mitis in the multi-species microenvironment. On the other hand, thioredoxin (TrxA) and other redox-regulating enzymes of H. pylori were less abundant in co-culture possibly suggesting reduced oxidative stress. Oxidative stress plays an important role in tissue damage and carcinogenesis. Using the in vitro co-culture model

  10. Surface-based morphometry reveals distinct cortical thickness and surface area profiles in Williams syndrome.

    PubMed

    Green, Tamar; Fierro, Kyle C; Raman, Mira M; Saggar, Manish; Sheau, Kristen E; Reiss, Allan L

    2016-04-01

    Morphometric investigations of brain volumes in Williams syndrome (WS) consistently show significant reductions in gray matter volume compared to controls. Cortical thickness (CT) and surface area (SA) are two constituent parts of cortical gray matter volume that are considered genetically distinguishable features of brain morphology. Yet, little is known about the independent contribution of cortical CT and SA to these volumetric differences in WS. Thus, our objectives were: (i) to evaluate whether the microdeletion in chromosome 7 associated with WS has a distinct effect on CT and SA, and (ii) to evaluate age-related variations in CT and SA within WS. We compared CT and SA values in 44 individuals with WS to 49 age- and sex-matched typically developing controls. Between-group differences in CT and SA were evaluated across two age groups: young (age range 6.6-18.9 years), and adults (age range 20.2-51.5 years). Overall, we found contrasting effects of WS on cortical thickness (increases) and surface area (decreases). With respect to brain topography, the between-group pattern of CT differences showed a scattered pattern while the between-group surface area pattern was widely distributed throughout the brain. In the adult subgroup, we observed a cluster of increases in cortical thickness in WS across the brain that was not observed in the young subgroup. Our findings suggest that extensive early reductions in surface area are the driving force for the overall reduction in brain volume in WS. The age-related cortical thickness findings might reflect delayed or even arrested development of specific brain regions in WS. © 2016 Wiley Periodicals, Inc.

  11. Medial prefrontal aberrations in major depressive disorder revealed by cytoarchitectonically informed voxel-based morphometry

    PubMed Central

    Bludau, Sebastian; Bzdok, Danilo; Gruber, Oliver; Kohn, Nils; Riedl, Valentin; Sorg, Christian; Palomero-Gallagher, Nicola; Müller, Veronika I.; Hoffstaedter, Felix; Amunts, Katrin; Eickhoff, Simon B.

    2017-01-01

    Objective The heterogeneous human frontal pole has been identified as a node in the dysfunctional network of major depressive disorder. The contribution of the medial (socio-affective) versus lateral (cognitive) frontal pole to major depression pathogenesis is currently unclear. The present study performs morphometric comparison of the microstructurally informed subdivisions of human frontal pole between depressed patients and controls using both uni- and multivariate statistics. Methods Multi-site voxel- and region-based morphometric MRI analysis of 73 depressed patients and 73 matched controls without psychiatric history. Frontal pole volume was first compared between depressed patients and controls by subdivision-wise classical morphometric analysis. In a second approach, frontal pole volume was compared by subdivision-naive multivariate searchlight analysis based on support vector machines. Results Subdivision-wise morphometric analysis found a significantly smaller medial frontal pole in depressed patients with a negative correlation of disease severity and duration. Histologically uninformed multivariate voxel-wise statistics provided converging evidence for structural aberrations specific to the microstructurally defined medial area of the frontal pole in depressed patients. Conclusions Across disparate methods, we demonstrated subregion specificity in the left medial frontal pole volume in depressed patients. Indeed, the frontal pole was shown to structurally and functionally connect to other key regions in major depression pathology like the anterior cingulate cortex and the amygdala via the uncinate fasciculus. Present and previous findings consolidate the left medial portion of the frontal pole as particularly altered in major depression. PMID:26621569

  12. Soft Tissue Morphometry of the Malleus–Incus Complex from Micro-CT Imaging

    PubMed Central

    Sim, Jae Hoon

    2008-01-01

    The malleus–incus complex (MIC) is unique to mammalian hearing. To develop a comprehensive biomechanical MIC model for the human middle ear, measurements regarding its anatomical features are a necessity. Micro-scale X-ray computed tomography (micro-CT) imaging, which is known to be a suitable method for imaging high-density tissue such as middle-ear ossicles and surrounding bones, is used in this study to determine the three-dimensional (3-D) morphometry of the soft tissue attachments of the MIC. The MIC morphometry is based on their 3-D reconstruction from micro-CT image slices with resolutions ranging from 10 to 20 μm. The suspensory ligament and tendon attachments of the malleus and the incus as well as the incudomalleal joint (IMJ), are quantified in terms of dimensions, positions, and orientations for four human cadaver temporal bones. The malleus principal frame, the incus principal frame, and the MIC principle frame are calculated and the morphometry is reported in relation to each of these frames for the first time. The resulting values show significant variation across ear samples, suggesting that models of the MIC should be based on individual anatomy. The IMJ morphometry dimensions appear to be proportional to the ossicular mass. The micro-CT imaging modality is a nondestructive and relatively fast method for obtaining soft tissue morphometry and provides accurate anatomical features in relation to the principal axes of bones. PMID:18311579

  13. An evaluation of volume-based morphometry for prediction of mild cognitive impairment and Alzheimer's disease

    PubMed Central

    Schmitter, Daniel; Roche, Alexis; Maréchal, Bénédicte; Ribes, Delphine; Abdulkadir, Ahmed; Bach-Cuadra, Meritxell; Daducci, Alessandro; Granziera, Cristina; Klöppel, Stefan; Maeder, Philippe; Meuli, Reto; Krueger, Gunnar

    2014-01-01

    Voxel-based morphometry from conventional T1-weighted images has proved effective to quantify Alzheimer's disease (AD) related brain atrophy and to enable fairly accurate automated classification of AD patients, mild cognitive impaired patients (MCI) and elderly controls. Little is known, however, about the classification power of volume-based morphometry, where features of interest consist of a few brain structure volumes (e.g. hippocampi, lobes, ventricles) as opposed to hundreds of thousands of voxel-wise gray matter concentrations. In this work, we experimentally evaluate two distinct volume-based morphometry algorithms (FreeSurfer and an in-house algorithm called MorphoBox) for automatic disease classification on a standardized data set from the Alzheimer's Disease Neuroimaging Initiative. Results indicate that both algorithms achieve classification accuracy comparable to the conventional whole-brain voxel-based morphometry pipeline using SPM for AD vs elderly controls and MCI vs controls, and higher accuracy for classification of AD vs MCI and early vs late AD converters, thereby demonstrating the potential of volume-based morphometry to assist diagnosis of mild cognitive impairment and Alzheimer's disease. PMID:25429357

  14. Considering total intracranial volume and other nuisance variables in brain voxel based morphometry in idiopathic PD.

    PubMed

    Crowley, Samuel; Huang, Haiqing; Tanner, Jared; Zhao, Qing; Schwab, Nadine A; Hizel, Loren; Ramon, Daniel; Brumback, Babette; Ding, Mingzhou; Price, Catherine C

    2017-01-09

    Voxel-based morphometry (VBM) studies of Parkinson's disease (PD), have yielded mixed results, possibly due to several studies not accounting for common nuisance variables (age, sex, and total intracranial volume [TICV]). TICV is particularly important because there is evidence for larger TICV in PD. We explored the influence of these covariates on VBM by 1) comparing PD patients and controls before adding covariates, after adding age and sex, and after adding age, sex and TICV, and 2) by comparing controls split into large and small TICV before and after controlling for TICV, with age and sex accounted for in both analyses. Experiment 1 consisted of 40 PD participants and 40 controls. Experiment 2 consisted of 88 controls median split by TICV. All participants completed an MRI on a 3 T scanner. TICV was calculated as gray + white + CSF from Freesurfer. VBM was performed on T1 images using an optimized VBM protocol. Volume differences were assessed using a voxel-wise GLM analysis. Clusters were considered significant at >10 voxels and p < .05 corrected for familywise error. Before controlling for covariates, PD showed reduced GM in temporal, occipital, and cerebellar regions. Controlling for age and sex did not affect the pattern of significance. Controlling for TICV reduced the size of the significant region although it still contained portions of bilateral temporal lobes, occipital lobes and cerebellum. The large TICV group showed reduced volume in temporal, parietal, and cerebellar areas. None of these differences survived controlling for TICV. This demonstrates that TICV influences VBM results independently from other factors. Controlling for TICV in VBM studies is recommended.

  15. Computed Tomography Measurement of Rib Cage Morphometry in Emphysema

    PubMed Central

    Sverzellati, Nicola; Colombi, Davide; Randi, Giorgia; Pavarani, Antonio; Silva, Mario; Walsh, Simon L.; Pistolesi, Massimo; Alfieri, Veronica; Chetta, Alfredo; Vaccarezza, Mauro; Vitale, Marco; Pastorino, Ugo

    2013-01-01

    Background Factors determining the shape of the human rib cage are not completely understood. We aimed to quantify the contribution of anthropometric and COPD-related changes to rib cage variability in adult cigarette smokers. Methods Rib cage diameters and areas (calculated from the inner surface of the rib cage) in 816 smokers with or without COPD, were evaluated at three anatomical levels using computed tomography (CT). CTs were analyzed with software, which allows quantification of total emphysema (emphysema%). The relationship between rib cage measurements and anthropometric factors, lung function indices, and %emphysema were tested using linear regression models. Results A model that included gender, age, BMI, emphysema%, forced expiratory volume in one second (FEV1)%, and forced vital capacity (FVC)% fit best with the rib cage measurements (R2 = 64% for the rib cage area variation at the lower anatomical level). Gender had the biggest impact on rib cage diameter and area (105.3 cm2; 95% CI: 111.7 to 98.8 for male lower area). Emphysema% was responsible for an increase in size of upper and middle CT areas (up to 5.4 cm2; 95% CI: 3.0 to 7.8 for an emphysema increase of 5%). Lower rib cage areas decreased as FVC% decreased (5.1 cm2; 95% CI: 2.5 to 7.6 for 10 percentage points of FVC variation). Conclusions This study demonstrates that simple CT measurements can predict rib cage morphometric variability and also highlight relationships between rib cage morphometry and emphysema. PMID:23935872

  16. MRI Study on Spinal Canal Morphometry: An Indian Study

    PubMed Central

    Kar, Maitreyee; Ishore, Kaushik; Saha, Pallab Kumar

    2017-01-01

    Introduction A large proportion of adults suffer from neck pain at some points of their life and show altered ranges of spinal canal morphometry in various studies. The differences in values are also seen due to genetic, hormonal and other factors too. Torg’s ratio is a widely accepted measurement to eliminate such discrepancies. The measurement of Space Available for Cord (SAC) is also gaining importance as spinal stenosis is a contributor to neck pain. Aim (1) To examine the cervical spinal canal and spinal cord morphometric determinants in symptomatic sub-Himalayan North Bengal population and to compare the obtained data with other populations; (2) To determine whether Torg’s ratio vary with gender or not; (3) To determine SAC values in symptomatic individuals. Materials and Methods Magnetic Resonance Imaging (MRI) based on midsagittal diameter of vertebral body, spinal canal, spinal cord and its Torg’s ratio and SAC value of the lower cervical spine (C3-C7) from 71 symptomatic adults were recorded at the Radiology Department of North Bengal Medical College and Hospital, Bengal, India. Individuals with any evidence of trauma, infection, neoplasia or any congenital anomalies related to spinal canal and below 18 years of age were excluded from the study. Results The average diameter for vertebral body was significantly larger in males. The average diameter for spinal canal, spinal cord and values of Torg’s ratio and SAC has no significant gender difference. But the mean value of Torg’s ratio is greater in females is due to smaller vertebral body size in females. Conclusion It is interpreted from our study that sagittal spinal canal diameter, Torg’s ratio and SAC value did not show any significant gender difference. But sagittal vertebral body’s diameter showed sexual dimorphism which influenced the mean value of Torg’s ratio. PMID:28658745

  17. Morphology and digitally aided morphometry of the human paracentral lobule.

    PubMed

    Spasojević, Goran; Malobabic, Slobodan; Pilipović-Spasojević, Olivera; Djukić-Macut, Nataša; Maliković, Aleksandar

    2013-02-01

    The human paracentral lobule, the junction of the precentral and postcentral gyri at the medial hemispheric surface, contains several important functional regions, and its variable morphology requires exact morphological and quantitativedata. In order to obtain precise data we investigated the morphology of the paracentral lobule and quantified its visible (extrasulcal) surface. This surface corresponds to commonly used magnetic resonance imaging scout images. We studied 84 hemispheres of adult persons (42 brains; 26 males and 16 females; 20-65 years) fixed in neutral formalin for at least 4 weeks. The medial hemispheric surface was photographed at standard distance and each digital photo was calibrated. Using the intercommissural line system (commissura anterior-commissura posterior or CA-CP line), we performed standardised measurements of the paracentral lobule. Exact determination of its boundaries and morphological types was followed by digital morphometry of its extrasulcal surface using AutoCAD software. We found two distinct morphological types of the human paracentral lobule: continuous type, which was predominant (95.2%), and rare segmented type (4.8%). In hemispheres with segmented cingulate sulcus we also found the short transitional lobulo-limbic gyrus (13.1%). The mean extrasulcal surface of the left paracentral lobule was significantly larger, both in males (left 6.79 cm2 vs. right 5.76 cm2) and in females (left 6.05 cm2 vs. right 5.16 cm2). However, even larger average surfaces in males were not significantly different than the same in females. Reported morphological and quantitative data will be useful during diagnostics and treatment of pathologies affecting the human paracentral lobule, and in further studies of its cytoarchitectonic and functional parcellations.

  18. Brain Gray Matter MRI Morphometry for Neuroprognostication After Cardiac Arrest.

    PubMed

    Silva, Stein; Peran, Patrice; Kerhuel, Lionel; Malagurski, Briguita; Chauveau, Nicolas; Bataille, Benoit; Lotterie, Jean Albert; Celsis, Pierre; Aubry, Florent; Citerio, Giuseppe; Jean, Betty; Chabanne, Russel; Perlbarg, Vincent; Velly, Lionel; Galanaud, Damien; Vanhaudenhuyse, Audrey; Fourcade, Olivier; Laureys, Steven; Puybasset, Louis

    2017-08-01

    We hypothesize that the combined use of MRI cortical thickness measurement and subcortical gray matter volumetry could provide an early and accurate in vivo assessment of the structural impact of cardiac arrest and therefore could be used for long-term neuroprognostication in this setting. Prospective cohort study. Five Intensive Critical Care Units affiliated to the University in Toulouse (France), Paris (France), Clermont-Ferrand (France), Liège (Belgium), and Monza (Italy). High-resolution anatomical T1-weighted images were acquired in 126 anoxic coma patients ("learning" sample) 16 ± 8 days after cardiac arrest and 70 matched controls. An additional sample of 18 anoxic coma patients, recruited in Toulouse, was used to test predictive model generalization ("test" sample). All patients were followed up 1 year after cardiac arrest. None. Cortical thickness was computed on the whole cortical ribbon, and deep gray matter volumetry was performed after automatic segmentation. Brain morphometric data were employed to create multivariate predictive models using learning machine techniques. Patients displayed significantly extensive cortical and subcortical brain volumes atrophy compared with controls. The accuracy of a predictive classifier, encompassing cortical and subcortical components, has a significant discriminative power (learning area under the curve = 0.87; test area under the curve = 0.96). The anatomical regions which volume changes were significantly related to patient's outcome were frontal cortex, posterior cingulate cortex, thalamus, putamen, pallidum, caudate, hippocampus, and brain stem. These findings are consistent with the hypothesis of pathologic disruption of a striatopallidal-thalamo-cortical mesocircuit induced by cardiac arrest and pave the way for the use of combined brain quantitative morphometry in this setting.

  19. Pelvic floor morphometry and function in women with and without puborectalis avulsion in the early postpartum period.

    PubMed

    Cyr, Marie-Pierre; Kruger, Jennifer; Wong, Vivien; Dumoulin, Chantale; Girard, Isabelle; Morin, Mélanie

    2017-03-01

    stiffness at 20-mm aperture (P ≤ .048). Significantly lower strength, speed of contraction, and endurance were also found in women with avulsion (P ≤ .005). They also presented more urinary incontinence symptoms (P = .040) whereas vaginal and bowel symptoms were found to be similar in the 2 groups. Pelvic Organ Prolapse Quantification revealed greater anterior compartment descent in women with avulsion (P ≤ .010). The impact of pelvic floor disorders on quality of life was found to be significantly higher in women with avulsion (P = .038). This study confirms that pelvic floor muscle morphometry and function are impaired in primiparous women with puborectalis avulsion in the early postpartum period. Moreover, it highlights specific muscle parameters that are altered such as passive properties, strength, speed of contraction, and endurance. Copyright © 2016 Elsevier Inc. All rights reserved.

  20. Effects of Omega-3 Fatty Acid Supplementation on Cognitive Functions and Neural Substrates: A Voxel-Based Morphometry Study in Aged Mice

    PubMed Central

    Cutuli, Debora; Pagani, Marco; Caporali, Paola; Galbusera, Alberto; Laricchiuta, Daniela; Foti, Francesca; Neri, Cristina; Spalletta, Gianfranco; Caltagirone, Carlo; Petrosini, Laura; Gozzi, Alessandro

    2016-01-01

    Human and experimental studies have revealed putative neuroprotective and pro-cognitive effects of omega-3 polyunsaturated fatty acids (n-3 PUFA) in aging, evidencing positive correlations between peripheral n-3 PUFA levels and regional grey matter (GM) volume, as well as negative correlations between dietary n-3 PUFA levels and cognitive deficits. We recently showed that n-3 PUFA supplemented aged mice exhibit better hippocampal-dependent mnesic functions, along with enhanced cellular plasticity and reduced neurodegeneration, thus supporting a role of n-3 PUFA supplementation in preventing cognitive decline during aging. To corroborate these initial results and develop new evidence on the effects of n-3 PUFA supplementation on brain substrates at macro-scale level, here we expanded behavioral analyses to the emotional domain (anxiety and coping skills), and carried out a fine-grained regional GM volumetric mapping by using high-resolution MRI-based voxel-based morphometry. The behavioral effects of 8 week n-3 PUFA supplementation were measured on cognitive (discriminative, spatial and social) and emotional (anxiety and coping) abilities of aged (19 month-old at the onset of study) C57B6/J mice. n-3 PUFA supplemented mice showed better mnesic performances as well as increased active coping skills. Importantly, these effects were associated with enlarged regional hippocampal, retrosplenial and prefrontal GM volumes, and with increased post mortem n-3 PUFA brain levels. These findings indicate that increased dietary n-3 PUFA intake in normal aging can improve fronto-hippocampal GM structure and function, an effect present also when the supplementation starts at late age. Our data are consistent with a protective role of n-3 PUFA supplementation in counteracting cognitive decline, emotional dysfunctions and brain atrophy. PMID:26973513

  1. Ocular refraction: heritability and genome-wide search for eye morphometry traits in an isolated Sardinian population.

    PubMed

    Biino, Ginevra; Palmas, Maria Antonietta; Corona, Carla; Prodi, Dionigio; Fanciulli, Manuela; Sulis, Roberta; Serra, Antonina; Fossarello, Maurizio; Pirastu, Mario

    2005-02-01

    No genes influencing oculometric phenotypes have yet been identified, despite it being well known that eye morphometry is involved in refraction and that genetics may play an important role. We have therefore performed a heritability analysis and genome-wide search (GWS) of biometric ocular traits in an isolated Sardinian population, assessing the genetic contribution and identifying the associated genetic loci. A complete eye examination including refraction and ocular biometry measurements such as axial length (AL), anterior chamber depth (ACD) and corneal curvature (CC), was performed on 789 subjects. Heritability analysis was carried out by means of parent-offspring regression and variance component models. Univariate and bivariate linkage analysis was performed by using 654 microsatellite markers spanning the genome. CC showed a mean heritability of 57%. AL and ACD were found to have significantly different variances (P<0.01) in males and females, so that heritability was calculated separately for each sex. AL had an estimated heritability in females of 31% and in males of 60%, whereas ACD had an estimated heritability of 47% in females and of 44% in males. In the GWS, the most suggestive evidence of linkage was identified on chromosome 2 for AL (LOD 2.64), on chromosome 1 for ACD (LOD 2.32) and on chromosomes 7, 2 and 3 for CC (LOD 2.50, 2.44 and 2.34, respectively). High heritability of eye morphometry traits was thus revealed. The identified loci are the first linkage signals available in ocular biometry. Notably, the observed significant differences in parental transmission deserve further study.

  2. A New Fiji-Based Algorithm That Systematically Quantifies Nine Synaptic Parameters Provides Insights into Drosophila NMJ Morphometry

    PubMed Central

    Wolf, Louis; Scheffer-de Gooyert, Jolanda M.; Monedero, Ignacio; Torroja, Laura; Coromina, Lluis; van der Laak, Jeroen A. W. M.; Schenck, Annette

    2016-01-01

    The morphology of synapses is of central interest in neuroscience because of the intimate relation with synaptic efficacy. Two decades of gene manipulation studies in different animal models have revealed a repertoire of molecules that contribute to synapse development. However, since such studies often assessed only one, or at best a few, morphological features at a given synapse, it remained unaddressed how different structural aspects relate to one another. Furthermore, such focused and sometimes only qualitative approaches likely left many of the more subtle players unnoticed. Here, we present the image analysis algorithm ‘Drosophila_NMJ_Morphometrics’, available as a Fiji-compatible macro, for quantitative, accurate and objective synapse morphometry of the Drosophila larval neuromuscular junction (NMJ), a well-established glutamatergic model synapse. We developed this methodology for semi-automated multiparametric analyses of NMJ terminals immunolabeled for the commonly used markers Dlg1 and Brp and showed that it also works for Hrp, Csp and Syt. We demonstrate that gender, genetic background and identity of abdominal body segment consistently and significantly contribute to variability in our data, suggesting that controlling for these parameters is important to minimize variability in quantitative analyses. Correlation and principal component analyses (PCA) were performed to investigate which morphometric parameters are inter-dependent and which ones are regulated rather independently. Based on nine acquired parameters, we identified five morphometric groups: NMJ size, geometry, muscle size, number of NMJ islands and number of active zones. Based on our finding that the parameters of the first two principal components hardly correlated with each other, we suggest that different molecular processes underlie these two morphometric groups. Our study sets the stage for systems morphometry approaches at the well-studied Drosophila NMJ. PMID:26998933

  3. Lake Morphometry for NHD Lakes in Souris Red Rainy Region 9 HUC

    EPA Pesticide Factsheets

    Lake morphometry metrics are known to influence productivity in lakes and are important for building various types of ecological and environmental models of lentic systems. The lake morphometry dataset included here contains estimates of Surface Area, Shoreline Length, Shoreline Development, Maximum Depth, Mean Depth, Lake Volume, Maximum Lake Length, Mean Lake Width, Maximum Lake Width, and Fetch for each of the ??lakepond?? waterbodies in the NHDPlus V2. The current release of the datasets is version 0.1 and future refinements to the data are expected.

  4. Lake Morphometry for NHD Lakes in the Upper Portion of the Missouri Region 10 HUC

    EPA Pesticide Factsheets

    Lake morphometry metrics are known to influence productivity in lakes and are important for building various types of ecological and environmental models of lentic systems. The lake morphometry dataset included here contains estimates of Surface Area, Shoreline Length, Shoreline Development, Maximum Depth, Mean Depth, Lake Volume, Maximum Lake Length, Mean Lake Width, Maximum Lake Width, and Fetch for each of the ??lakepond?? waterbodies in the NHDPlus V2. The current release of the datasets is version 0.1 and future refinements to the data are expected.

  5. Lake Morphometry for NHD Lakes in Upper Colorado Region 14 HUC

    EPA Pesticide Factsheets

    Lake morphometry metrics are known to influence productivity in lakes and are important for building various types of ecological and environmental models of lentic systems. The lake morphometry dataset included here contains estimates of Surface Area, Shoreline Length, Shoreline Development, Maximum Depth, Mean Depth, Lake Volume, Maximum Lake Length, Mean Lake Width, Maximum Lake Width, and Fetch for each of the ??lakepond?? waterbodies in the NHDPlus V2. The current release of the datasets is version 0.1 and future refinements to the data are expected.

  6. Lake Morphometry for NHD Lakes in Upper Mississippi Region 7 HUC

    EPA Pesticide Factsheets

    Lake morphometry metrics are known to influence productivity in lakes and are important for building various types of ecological and environmental models of lentic systems. The lake morphometry dataset included here contains estimates of Surface Area, Shoreline Length, Shoreline Development, Maximum Depth, Mean Depth, Lake Volume, Maximum Lake Length, Mean Lake Width, Maximum Lake Width, and Fetch for each of the ??lakepond?? waterbodies in the NHDPlus V2. The current release of the datasets is version 0.1 and future refinements to the data are expected.

  7. Lake Morphometry for NHD Lakes in Great Basin Region 16 HUC

    EPA Pesticide Factsheets

    Lake morphometry metrics are known to influence productivity in lakes and are important for building various types of ecological and environmental models of lentic systems. The lake morphometry dataset included here contains estimates of Surface Area, Shoreline Length, Shoreline Development, Maximum Depth, Mean Depth, Lake Volume, Maximum Lake Length, Mean Lake Width, Maximum Lake Width, and Fetch for each of the ??lakepond?? waterbodies in the NHDPlus V2. The current release of the datasets is version 0.1 and future refinements to the data are expected.

  8. Lake Morphometry for NHD Lakes in Texas-Gulf Region 12 HUC

    EPA Pesticide Factsheets

    Lake morphometry metrics are known to influence productivity in lakes and are important for building various types of ecological and environmental models of lentic systems. The lake morphometry dataset included here contains estimates of Surface Area, Shoreline Length, Shoreline Development, Maximum Depth, Mean Depth, Lake Volume, Maximum Lake Length, Mean Lake Width, Maximum Lake Width, and Fetch for each of the ??lakepond?? waterbodies in the NHDPlus V2. The current release of the datasets is version 0.1 and future refinements to the data are expected.

  9. Lake Morphometry for NHD Lakes in Lower Mississippi Region 8 HUC

    EPA Pesticide Factsheets

    Lake morphometry metrics are known to influence productivity in lakes and are important for building various types of ecological and environmental models of lentic systems. The lake morphometry dataset included here contains estimates of Surface Area, Shoreline Length, Shoreline Development, Maximum Depth, Mean Depth, Lake Volume, Maximum Lake Length, Mean Lake Width, Maximum Lake Width, and Fetch for each of the ??lakepond?? waterbodies in the NHDPlus V2. The current release of the datasets is version 0.1 and future refinements to the data are expected.

  10. Lake Morphometry for NHD Lakes in Mid-Atlantic Region 2 HUC

    EPA Pesticide Factsheets

    Lake morphometry metrics are known to influence productivity in lakes and are important for building various types of ecological and environmental models of lentic systems. The lake morphometry dataset included here contains estimates of Surface Area, Shoreline Length, Shoreline Development, Maximum Depth, Mean Depth, Lake Volume, Maximum Lake Length, Mean Lake Width, Maximum Lake Width, and Fetch for each of the ??lakepond?? waterbodies in the NHDPlus V2. The current release of the datasets is version 0.1 and future refinements to the data are expected.

  11. Lake Morphometry for NHD Lakes in North East Region 1 HUC

    EPA Pesticide Factsheets

    Lake morphometry metrics are known to influence productivity in lakes and are important for building various types of ecological and environmental models of lentic systems. The lake morphometry dataset included here contains estimates of Surface Area, Shoreline Length, Shoreline Development, Maximum Depth, Mean Depth, Lake Volume, Maximum Lake Length, Mean Lake Width, Maximum Lake Width, and Fetch for each of the ??lakepond?? waterbodies in the NHDPlus V2. The current release of the datasets is version 0.1 and future refinements to the data are expected.

  12. Lake Morphometry for NHD Lakes in Pacific Northwest Region 17 HUC

    EPA Pesticide Factsheets

    Lake morphometry metrics are known to influence productivity in lakes and are important for building various types of ecological and environmental models of lentic systems. The lake morphometry dataset included here contains estimates of Surface Area, Shoreline Length, Shoreline Development, Maximum Depth, Mean Depth, Lake Volume, Maximum Lake Length, Mean Lake Width, Maximum Lake Width, and Fetch for each of the ??lakepond?? waterbodies in the NHDPlus V2. The current release of the datasets is version 0.1 and future refinements to the data are expected.

  13. Lake Morphometry for NHD Lakes in Rio Grande Region 13 HUC

    EPA Pesticide Factsheets

    Lake morphometry metrics are known to influence productivity in lakes and are important for building various types of ecological and environmental models of lentic systems. The lake morphometry dataset included here contains estimates of Surface Area, Shoreline Length, Shoreline Development, Maximum Depth, Mean Depth, Lake Volume, Maximum Lake Length, Mean Lake Width, Maximum Lake Width, and Fetch for each of the ??lakepond?? waterbodies in the NHDPlus V2. The current release of the datasets is version 0.1 and future refinements to the data are expected.

  14. Lake Morphometry for NHD Lakes in Great Lakes Region 4 HUC

    EPA Pesticide Factsheets

    Lake morphometry metrics are known to influence productivity in lakes and are important for building various types of ecological and environmental models of lentic systems. The lake morphometry dataset included here contains estimates of Surface Area, Shoreline Length, Shoreline Development, Maximum Depth, Mean Depth, Lake Volume, Maximum Lake Length, Mean Lake Width, Maximum Lake Width, and Fetch for each of the ??lakepond?? waterbodies in the NHDPlus V2. The current release of the datasets is version 0.1 and future refinements to the data are expected.

  15. Lake Morphometry for NHD Lakes in the Lower Portion of the Missouri Region 10 HUC

    EPA Pesticide Factsheets

    Lake morphometry metrics are known to influence productivity in lakes and are important for building various types of ecological and environmental models of lentic systems. The lake morphometry dataset included here contains estimates of Surface Area, Shoreline Length, Shoreline Development, Maximum Depth, Mean Depth, Lake Volume, Maximum Lake Length, Mean Lake Width, Maximum Lake Width, and Fetch for each of the ??lakepond?? waterbodies in the NHDPlus V2. The current release of the datasets is version 0.1 and future refinements to the data are expected.

  16. Lake Morphometry for NHD Lakes in Lower Colorado Region 15 HUC

    EPA Pesticide Factsheets

    Lake morphometry metrics are known to influence productivity in lakes and are important for building various types of ecological and environmental models of lentic systems. The lake morphometry dataset included here contains estimates of Surface Area, Shoreline Length, Shoreline Development, Maximum Depth, Mean Depth, Lake Volume, Maximum Lake Length, Mean Lake Width, Maximum Lake Width, and Fetch for each of the ??lakepond?? waterbodies in the NHDPlus V2. The current release of the datasets is version 0.1 and future refinements to the data are expected.

  17. Lake Morphometry for NHD Lakes in Arkansas White Red Region 11 HUC

    EPA Pesticide Factsheets

    Lake morphometry metrics are known to influence productivity in lakes and are important for building various types of ecological and environmental models of lentic systems. The lake morphometry dataset included here contains estimates of Surface Area, Shoreline Length, Shoreline Development, Maximum Depth, Mean Depth, Lake Volume, Maximum Lake Length, Mean Lake Width, Maximum Lake Width, and Fetch for each of the ??lakepond?? waterbodies in the NHDPlus V2. The current release of the datasets is version 0.1 and future refinements to the data are expected.

  18. Nuclear morphometry in canine acanthomatous ameloblastomas and squamous cell carcinomas.

    PubMed

    Martano, M; Damiano, S; Restucci, B; Paciello, O; Russo, V; Maiolino, P

    2006-01-01

    The aim of this study was to evaluate whether morphometrical analysis can be of diagnostic value for canine acanthomatous ameloblastoma. We calculated, by means of an automated image analyser, some morphometric nuclear parameters, in particular: mean nuclear area (MNA), mean nuclear perimeter (MNP), maximum and minimum diameters (MDx and MDm) coefficient of variation of the nuclear area (NACV), largest to smallest dimension ratio (LS ratio), and form factor (FF), in 8 canine acanthomatous ameloblastomas, and we compared these morphometric data to those of 13 squamous cell carcinomas of canine gingiva. The results indicated a progressive increase of the MNA, NACV, MNP and MDm proceeding from acanthomatous ameloblastomas (MNA: 42.11+/-8.74; NACV: 28,36+/-7,23; MNP: 24.18+/- 2.68; MDm: 5.69+/-0.49) to squamous cell carcinomas (MNA:49,69+/-9,10; NACV: 30,89+/-7,75; MNP: 25.63+/-2.54; MDm: 6.64+/-0.73). On the contrary, the LS ratio and the FF resulted greater in acanthomatous ameloblastomas (LS ratio: 1,63+/-0,12; FF: 1,13+/-0,002) than in SCCs (LS ratio: 1,40+/-0,12; FF:0.91+/-0.38). Moreover, the MNA, MNP,MDx and MDm resulted similar (MNA: p=0.89; MNP: p=0,65; MDm: p=0,16; MDx: p=0,13) in a subset of four acanthomatous ameloblastomas with cellular atypia (MNA:49,01+/-6,88; MNP: 26,28+/-1,99; MDm: 6.08+/-0.41; MDx: 10.18+/-0.88) and in squamous cell carcinomas (MNA:49.69+/-9,10; MNP: 25.63+/-2.54; MDm: 6.64+/-0.73; MDx: 9.26+/-1.05). While the NACV values resulted higher in typical acanthomatous ameloblastoma (29,99+/-6,06) than in atypical acanthomatous ameloblastoma (26,74+/-8,84) and similar to those of the SCCs (30,89+/-7,75). These results seem to confirm that acanthomatous ameloblastoma is a malignant or potentially malignant lesion and emphasizes that nuclear morphometry analysis can be an useful diagnostic and prognostic method in canine oral pathology.

  19. Hippocampal substructural vulnerability to sleep disturbance and cognitive impairment in patients with chronic primary insomnia: magnetic resonance imaging morphometry.

    PubMed

    Joo, Eun Yeon; Kim, Hosung; Suh, Sooyeon; Hong, Seung Bong

    2014-07-01

    Despite compelling evidence from animal studies indicating hippocampal subfield-specific vulnerability to poor sleep quality and related cognitive impairment, there have been no human magnetic resonance imaging (MRI) studies investigating the relationship between hippocampal subfield volume and sleep disturbance. Our aim was to investigate the pattern of volume changes across hippocampal subfields in patients with primary insomnia relative to controls. Pointwise morphometry allowed for volume measurements of hippocampal regions on T1-weighted MRI. University hospital. Twenty-seven unmedicated patients (age: 51.2 ± 9.6 y) and 30 good sleepers as controls (50.4 ± 7.1 y). N/A. We compared hippocampal subfield volumes between patients and controls and correlated volume with clinical and neuropsychological features in patients. Patients exhibited bilateral atrophy across all hippocampal subfields (P < 0.05 corrected). Cornu ammonis (CA) 1 subfield atrophy was associated with worse sleep quality (higher Pittsburgh Sleep Quality Index and higher arousal index of polysomnography) (r < -0.45, P < 0.005). The volume of the combined region, including the dentate gyrus (DG) and CA3-4, negatively correlated with verbal memory, verbal information processing, and verbal fluency in patients (|r| > 0.45, P < 0.05). Hemispheric volume asymmetry of this region (left smaller than right) was associated with impaired verbal domain functions (r = 0.50, P < 0.005). Hippocampal subfield atrophy in chronic insomnia suggests reduced neurogenesis in the dentate gyrus (DG) and neuronal loss in the cornu ammonis (CA) subfields in conditions of sleep fragmentation and related chronic stress condition. Atrophy in the CA3-4-DG region was associated with impaired cognitive functions in patients. These observations may provide insight into pathophysiological mechanisms that make patients with chronic sleep disturbance vulnerable to cognitive impairment. Joo EY, Kim H, Suh S, Hong SB. Hippocampal

  20. Differences in Cell Morphometry, Cell Wall Topography and Gp70 Expression Correlate with the Virulence of Sporothrix brasiliensis Clinical Isolates

    PubMed Central

    Castro, Rafaela A.; Kubitschek-Barreira, Paula H.; Teixeira, Pedro A. C.; Sanches, Glenda F.; Teixeira, Marcus M.; Quintella, Leonardo P.; Almeida, Sandro R.; Costa, Rosane O.; Camargo, Zoilo P.; Felipe, Maria S. S.; de Souza, Wanderley; Lopes-Bezerra, Leila M.

    2013-01-01

    Sporotrichosis is a chronic infectious disease affecting both humans and animals. For many years, this subcutaneous mycosis had been attributed to a single etiological agent; however, it is now known that this taxon consists of a complex of at least four pathogenic species, including Sporothrix schenckii and Sporothrix brasiliensis. Gp70 was previously shown to be an important antigen and adhesin expressed on the fungal cell surface and may have a key role in immunomodulation and host response. The aim of this work was to study the virulence, morphometry, cell surface topology and gp70 expression of clinical isolates of S. brasiliensis compared with two reference strains of S. schenckii. Several clinical isolates related to severe human cases or associated with the Brazilian zoonotic outbreak of sporotrichosis were genotyped and clustered as S. brasiliensis. Interestingly, in a murine subcutaneous model of sporotrichosis, these isolates showed a higher virulence profile compared with S. schenckii. A single S. brasiliensis isolate from an HIV-positive patient not only showed lower virulence but also presented differences in cell morphometry, cell wall topography and abundant gp70 expression compared with the virulent isolates. In contrast, the highly virulent S. brasiliensis isolates showed reduced levels of cell wall gp70. These observations were confirmed by the topographical location of the gp70 antigen using immunoelectromicroscopy in both species. In addition, the gp70 molecule was sequenced and identified using mass spectrometry, and the sequenced peptides were aligned into predicted proteins using Blastp with the S. schenckii and S. brasiliensis genomes. PMID:24116065

  1. Increased gray matter density in the parietal cortex of mathematicians: a voxel-based morphometry study.

    PubMed

    Aydin, K; Ucar, A; Oguz, K K; Okur, O O; Agayev, A; Unal, Z; Yilmaz, S; Ozturk, C

    2007-01-01

    The training to acquire or practicing to perform a skill, which may lead to structural changes in the brain, is called experience-dependent structural plasticity. The main purpose of this cross-sectional study was to investigate the presence of experience-dependent structural plasticity in mathematicians' brains, which may develop after long-term practice of mathematic thinking. Twenty-six volunteer mathematicians, who have been working as academicians, were enrolled in the study. We applied an optimized method of voxel-based morphometry in the mathematicians and the age- and sex-matched control subjects. We assessed the gray and white matter density differences in mathematicians and the control subjects. Moreover, the correlation between the cortical density and the time spent as an academician was investigated. We found that cortical gray matter density in the left inferior frontal and bilateral inferior parietal lobules of the mathematicians were significantly increased compared with the control subjects. Furthermore, increase in gray matter density in the right inferior parietal lobule of the mathematicians was strongly correlated with the time spent as an academician (r = 0.84; P < .01). Left-inferior frontal and bilateral parietal regions are involved in arithmetic processing. Inferior parietal regions are also involved in high-level mathematic thinking, which requires visuospatial imagery, such as mental creation and manipulation of 3D objects. The voxel-based morphometric analysis of mathematicians' brains revealed increased gray matter density in the cortical regions related to mathematic thinking. The correlation between cortical density increase and the time spent as an academician suggests experience-dependent structural plasticity in mathematicians' brains.

  2. Censoring Distances Based on Labeled Cortical Distance Maps in Cortical Morphometry

    PubMed Central

    Ceyhan, Elvan; Nishino, Tomoyuki; Alexopolous, Dimitrios; Todd, Richard D.; Botteron, Kelly N.; Miller, Michael I.; Ratnanather, J. Tilak

    2013-01-01

    It has been demonstrated that shape differences in cortical structures may be manifested in neuropsychiatric disorders. Such morphometric differences can be measured by labeled cortical distance mapping (LCDM) which characterizes the morphometry of the laminar cortical mantle of cortical structures. LCDM data consist of signed/labeled distances of gray matter (GM) voxels with respect to GM/white matter (WM) surface. Volumes and other summary measures for each subject and the pooled distances can help determine the morphometric differences between diagnostic groups, however they do not reveal all the morphometric information contained in LCDM distances. To extract more information from LCDM data, censoring of the pooled distances is introduced for each diagnostic group where the range of LCDM distances is partitioned at a fixed increment size; and at each censoring step, the distances not exceeding the censoring distance are kept. Censored LCDM distances inherit the advantages of the pooled distances but also provide information about the location of morphometric differences which cannot be obtained from the pooled distances. However, at each step, the censored distances aggregate, which might confound the results. The influence of data aggregation is investigated with an extensive Monte Carlo simulation analysis and it is demonstrated that this influence is negligible. As an illustrative example, GM of ventral medial prefrontal cortices (VMPFCs) of subjects with major depressive disorder (MDD), subjects at high risk (HR) of MDD, and healthy control (Ctrl) subjects are used. A significant reduction in laminar thickness of the VMPFC in MDD and HR subjects is observed compared to Ctrl subjects. Moreover, the GM LCDM distances (i.e., locations with respect to the GM/WM surface) for which these differences start to occur are determined. The methodology is also applicable to LCDM-based morphometric measures of other cortical structures affected by disease. PMID:24133482

  3. Effects of HIV and childhood trauma on brain morphometry and neurocognitive function.

    PubMed

    Spies, Georgina; Ahmed-Leitao, Fatima; Fennema-Notestine, Christine; Cherner, Mariana; Seedat, Soraya

    2016-04-01

    A wide spectrum of neurocognitive deficits characterises HIV infection in adults. HIV infection is additionally associated with morphological brain abnormalities affecting neural substrates that subserve neurocognitive function. Early life stress (ELS) also has a direct influence on brain morphology. However, the combined impact of ELS and HIV on brain structure and neurocognitive function has not been examined in an all-female sample with advanced HIV disease. The present study examined the effects of HIV and childhood trauma on brain morphometry and neurocognitive function. Structural data were acquired using a 3T Magnetom MRI scanner, and a battery of neurocognitive tests was administered to 124 women: HIV-positive with ELS (n = 32), HIV-positive without ELS (n = 30), HIV-negative with ELS (n = 31) and HIV-negative without ELS (n = 31). Results revealed significant group volumetric differences for right anterior cingulate cortex (ACC), bilateral hippocampi, corpus callosum, left and right caudate and left and right putamen. Mean regional volumes were lowest in HIV-positive women with ELS compared to all other groups. Although causality cannot be inferred, findings also suggest that alterations in the left frontal lobe, right ACC, left hippocampus, corpus callosum, left and right amygdala and left caudate may be associated with poorer neurocognitive performance in the domains of processing speed, attention/working memory, abstraction/executive functions, motor skills, learning and language/fluency with these effects more pronounced in women living with both HIV and childhood trauma. This study highlights the potential contributory role of childhood trauma to brain alterations and neurocognitive decline in HIV-infected individuals.

  4. Effects of HIV and childhood trauma on brain morphometry and neurocognitive function

    PubMed Central

    Spies, Georgina; Ahmed-Leitao, Fatima; Fennema-Notestine, Christine; Cherner, Mariana; Seedat, Soraya

    2016-01-01

    A wide spectrum of neurocognitive deficits characterise HIV infection in adults. HIV infection is additionally associated with morphological brain abnormalities affecting neural substrates that subserve neurocognitive function. Early life stress (ELS) also has a direct influence on brain morphology. However, the combined impact of ELS and HIV on brain structure and neurocognitive function has not been examined in an all-female sample with advanced HIV disease. The present study examined the effects of HIV and childhood trauma on brain morphometry and neurocognitive function. Structural data were acquired using a 3T Magnetom MRI scanner and a battery of neurocognitive tests was administered to 124 women; HIV positive with ELS (n = 32), HIV positive without ELS (n = 30), HIV negative with ELS (n = 31), HIV negative without ELS (n = 31). Results revealed significant group volumetric differences for right anterior cingulate cortex (ACC), bilateral hippocampi, corpus callosum, left and right caudate, and left and right putamen. Mean regional volumes were lowest in HIV positive women with ELS compared to all other groups. Although causality cannot be inferred, findings also suggest that alterations in the left frontal lobe, right ACC, left hippocampus, corpus callosum, left and right amygdala, and left caudate may be associated with poorer neurocognitive performance in the domains of processing speed, attention/working memory, abstraction/executive functions, motor skills, learning, and language/fluency with these effects more pronounced in women living with both HIV and childhood trauma. This study highlights the potential contributory role of childhood trauma to brain alterations and neurocognitive decline in HIV infected individuals. PMID:26424107

  5. Morphometry and subpopulation structure of Holstein bull spermatozoa: variations in ejaculates and cryopreservation straws

    PubMed Central

    Valverde, Anthony; Arenán, Héctor; Sancho, María; Contell, Jesús; Yániz, Jesús; Fernández, Alejandro; Soler, Carles

    2016-01-01

    Sperm quality is evaluated for the calculation of sperm dosage in artificial reproductive programs. The most common parameter used is motility, but morphology has a higher potential as a predictor of genetic quality. Morphometry calculations from CASA-Morph technology improve morphological evaluation and allow mathematical approaches to the problem. Semen from 28 Holstein bulls was collected by artificial vagina, and several ejaculates were studied. After general evaluation, samples were diluted, packaged in 0.25 ml straws, and stored in liquid nitrogen. Two straws per sample were thawed, and slides were processed and stained with Diff-Quik. Samples were analyzed by a CASA-Morph system for eight morphometric parameters. In addition to the “classical” statistical approach, based on variance analysis (revealing differences between animals, ejaculates, and straws), principal component (PC) analysis showed that the variables were grouped into PC1, related to size, and PC2 to shape. Subpopulation structure analysis showed four groups, namely, big, small, short, and narrow from their dominant characteristics, representing 31.0%, 27.3%, 24.1%, and 17.7% of the total population, respectively. The distributions varied between animals and ejaculates, but between straws, there were no differences in only four animals. This modern approach of considering an ejaculate sperm population as divided into subpopulations reflecting quantifiable parameters generated by CASA-Morph systems technology opens a new view on sperm function. This is the first study applying this approach to evaluate different ejaculates and straws from the same individual. More work must be done to improve seminal dose calculations in assisted reproductive programs. PMID:27678464

  6. Surface morphology and morphometry of rat alveolar macrophages after ozone exposure

    SciTech Connect

    Dormans, J.A.; Rombout, P.J.; van Loveren, H. )

    1990-09-01

    As the ultrastructural data on the effects of ozone on pulmonary alveolar macrophages (PAM) are lacking, transmission (TEM) and scanning (SEM) electron microscopy were performed on rat PAM present in alveolar lavages following exposure to ozone. Rats were continuously exposed for 7 d to ozone concentrations ranging from 0.25 to 1.50 mg/m3 for 7 d followed by a 5-d recovery period. Additionally, morphometry on lung sections was performed to quantitate PAM. In a second experiment rats were continuously exposed to 1.50 mg O3/m3 for 1, 3, 5, or 7 d. To study the influence of concurrent ozone exposure and lung infection, due to Listeria monocytogenes, rats were exposed for 7 d to 1.50 mg O3/m3 after a Listeria infection. The surface area of lavaged control PAM was uniformly covered with ruffles as shown by SEM and TEM. Exposure to 0.5 mg ozone/m3 for 7 d resulted in cells partly covered with microvilli and blebs in addition to normal ruffles. The number of large size PAM increased with an increase in ozone concentration. After 1 d of exposure, normal-appearing as well as many small macrophages with ruffles and scattered lymphocytes were seen. Lavage samples taken after 5 or 7 d of exposure showed an identical cell composition to that taken after 3 d of exposure. After Listeria infection alone, lavage samples consisted of mainly lymphocytes and some macrophages. Small quantitative changes, such as an increase in the number of polymorphonuclear neutrophils and large-size PAM, occurred in lavages after ozone exposure and infection with L. monocytogenes. Morphometric examination of lung sections revealed a concentration-related increase in the number of PAM, even in animals exposed to 0.25 mg ozone/m3 for 7 d. Centriacinar regions were more severely affected than other regions of lung tissue.

  7. Sperm ultrastructure, morphometry, and abnormal morphology in American black bears (Ursus americanus).

    PubMed

    Brito, L F C; Sertich, P L; Stull, G B; Rives, W; Knobbe, M

    2010-11-01

    The objective of this study was to describe sperm ultrastructure, morphometry, and abnormal morphology in American black bears. Electroejaculation was successful in 53.8% (7/13) of the attempts, but urine contamination was common. Epididymal sperm samples were also obtained from five bears. Sperm had a paddle-like head shape and the ultrastructure was similar to that of most other mammals. The most striking particularity of black bear sperm ultrastructure was a tightening of the nucleus in the equatorial region. Although the differences were not significant in all bears, the overall decrease in sperm nucleus dimensions during transport from the caput epididymis to the cauda suggested increasing compaction of the nucleus during maturation. For ejaculated sperm, nucleus length, width, and base width were 4.9, 3.7, and 1.8 μm, respectively, whereas sperm head length, width, and base width were 6.6, 4.8, and 2.3 μm, and midpiece, tail (including midpiece), and total sperm lengths were 9.8, 68.8, and 75.3 μm. Evaluation of sperm cytoplasmic droplets in the epididymis revealed that proximal droplets start migrating toward a distal position in the caput epididymis and that the process was mostly completed by the time sperm reached the cauda epididymis. The proportion of morphologically normal sperm in the ejaculate was 35.6%; the most prevalent sperm defects were distal cytoplasmic droplets and bent/coiled tails. The morphology of abnormal sperm and the underlying ultrastructural defects were similar to that in other large domestic animals thus suggesting similar underlying pathogenesis of specific sperm defects and similar effects on fertility.

  8. Morphometry and subpopulation structure of Holstein bull spermatozoa: variations in ejaculates and cryopreservation straws.

    PubMed

    Valverde, Anthony; Arenán, Héctor; Sancho, María; Contell, Jesús; Yániz, Jesús; Fernández, Alejandro; Soler, Carles

    2016-01-01

    Sperm quality is evaluated for the calculation of sperm dosage in artificial reproductive programs. The most common parameter used is motility, but morphology has a higher potential as a predictor of genetic quality. Morphometry calculations from CASA-Morph technology improve morphological evaluation and allow mathematical approaches to the problem. Semen from 28 Holstein bulls was collected by artificial vagina, and several ejaculates were studied. After general evaluation, samples were diluted, packaged in 0.25 ml straws, and stored in liquid nitrogen. Two straws per sample were thawed, and slides were processed and stained with Diff-Quik. Samples were analyzed by a CASA-Morph system for eight morphometric parameters. In addition to the "classical" statistical approach, based on variance analysis (revealing differences between animals, ejaculates, and straws), principal component (PC) analysis showed that the variables were grouped into PC1, related to size, and PC2 to shape. Subpopulation structure analysis showed four groups, namely, big, small, short, and narrow from their dominant characteristics, representing 31.0%, 27.3%, 24.1%, and 17.7% of the total population, respectively. The distributions varied between animals and ejaculates, but between straws, there were no differences in only four animals. This modern approach of considering an ejaculate sperm population as divided into subpopulations reflecting quantifiable parameters generated by CASA-Morph systems technology opens a new view on sperm function. This is the first study applying this approach to evaluate different ejaculates and straws from the same individual. More work must be done to improve seminal dose calculations in assisted reproductive programs.

  9. Brain morphometry shows effects of long-term musical practice in middle-aged keyboard players

    PubMed Central

    Gärtner, H.; Minnerop, M.; Pieperhoff, P.; Schleicher, A.; Zilles, K.; Altenmüller, E.; Amunts, K.

    2013-01-01

    To what extent does musical practice change the structure of the brain? In order to understand how long-lasting musical training changes brain structure, 20 male right-handed, middle-aged professional musicians and 19 matched controls were investigated. Among the musicians, 13 were pianists or organists with intensive practice regimes. The others were either music teachers at schools or string instrumentalists, who had studied the piano at least as a subsidiary subject, and practiced less intensively. The study was based on T1-weighted MR images, which were analyzed using deformation-based morphometry. Cytoarchitectonic probabilistic maps of cortical areas and subcortical nuclei as well as myeloarchitectonic maps of fiber tracts were used as regions of interest to compare volume differences in the brains of musicians and controls. In addition, maps of voxel-wise volume differences were computed and analyzed. Musicians showed a significantly better symmetric motor performance as well as a greater capability of controlling hand independence than controls. Structural MRI-data revealed significant volumetric differences between the brains of keyboard players, who practiced intensively and controls in right sensorimotor areas and the corticospinal tract as well as in the entorhinal cortex and the left superior parietal lobule. Moreover, they showed also larger volumes in a comparable set of regions than the less intensively practicing musicians. The structural changes in the sensory and motor systems correspond well to the behavioral results, and can be interpreted in terms of plasticity as a result of intensive motor training. Areas of the superior parietal lobule and the entorhinal cortex might be enlarged in musicians due to their special skills in sight-playing and memorizing of scores. In conclusion, intensive and specific musical training seems to have an impact on brain structure, not only during the sensitive period of childhood but throughout life. PMID

  10. Sports and brain morphology - a voxel-based morphometry study with endurance athletes and martial artists.

    PubMed

    Schlaffke, L; Lissek, S; Lenz, M; Brüne, M; Juckel, G; Hinrichs, T; Platen, P; Tegenthoff, M; Schmidt-Wilcke, T

    2014-02-14

    Physical exercises and motor skill learning have been shown to induce changes in regional brain morphology, this has been demonstrated for various activities and tasks. Also individuals with special skills show differences in regional brain morphology. This has been indicated for professional musicians, London taxi drivers, as well as for athletes like dancers, golfers and judokas. However little is known about whether sports with different metabolic profiles (aerobic vs. anaerobic) are associated with different patterns of altered brain morphology. In this cross-sectional study we investigated two groups of high-performance athletes, one group performing sports that are thought to be mainly aerobic, and one group performing sports known to have intermittent phases of anaerobic metabolism. Using high-resolution structural imaging and voxel-based morphometry (VBM), we investigated a group of 26 male athletes consisting of 13 martial artists and 13 endurance athletes as well as a group of non-exercising men (n=13). VBM analyses revealed higher gray matter (GM) volumes in the supplementary motor area/dorsal premotor cortex (BA 6) in both athlete groups as compared to the control group. In addition, endurance athletes showed significantly higher GM volume in the medial temporal lobe (MTL), specifically in the hippocampus and parahippocampal gyrus, which was not seen in the martial arts group. Our data suggest that high-performance sports are associated with changes in regional brain morphology in areas implicated in motor planning and motor learning. In addition high-level endurance sports seem to affect MTL structures, areas that have previously been shown to be modulated by aerobic exercise. Copyright © 2013 IBRO. Published by Elsevier Ltd. All rights reserved.

  11. Crystal structure of CobK reveals strand-swapping between Rossmann-fold domains and molecular basis of the reduced precorrin product trap

    NASA Astrophysics Data System (ADS)

    Gu, Shuang; Sushko, Oleksandr; Deery, Evelyne; Warren, Martin J.; Pickersgill, Richard W.

    2015-11-01

    CobK catalyzes the essential reduction of the precorrin ring in the cobalamin biosynthetic pathway. The crystal structure of CobK reveals that the enzyme, despite not having the signature sequence, comprises two Rossmann fold domains which bind coenzyme and substrate respectively. The two parallel β-sheets have swapped their last β-strands giving a novel sheet topology which is an interesting variation on the Rossmann-fold. The trapped ternary complex with coenzyme and product reveals five conserved basic residues that bind the carboxylates of the tetrapyrrole tightly anchoring the product. A loop, disordered in both the apoenzyme and holoenzyme structures, closes around the product further tightening binding. The structure is consistent with a mechanism involving protonation of C18 and pro-R hydride transfer from NADPH to C19 of precorrin-6A and reveals the interactions responsible for the specificity of CobK. The almost complete burial of the reduced precorrin product suggests a remarkable form of metabolite channeling where the next enzyme in the biosynthetic pathway triggers product release.

  12. Long-term nitrogen fertilization of paddy soil shifts iron-reducing microbial community revealed by RNA-13C-acetate probing coupled with pyrosequencing

    PubMed Central

    Ding, Long-Jun; Su, Jian-Qiang; Xu, Hui-Juan; Jia, Zhong-Jun; Zhu, Yong-Guan

    2015-01-01

    Iron reduction is an important biogeochemical process in paddy soils, yet little is known about the microbial coupling between nitrogen and iron reduction. Here, we investigated the shift of acetate-metabolizing iron-reducers under long-term nitrogen fertilization using 13C-acetate-based ribosomal RNA (rRNA)-stable isotope probing (SIP) and pyrosequencing in an incubation experiment, and the shift of putative iron-reducers in original field samples were investigated by 16S rRNA gene-based pyrosequencing. During SIP incubations, in the presence of iron(III) oxyhydroxides, more iron(II) formation and less methane production were detected in nitrogen-fertilized (N) compared with non-fertilized (NF) soil. In 13C-rRNA from microcosms amended with ferrihydrite (FER), Geobacter spp. were the important active iron-reducers in both soils, and labeled to a greater extent in N (31% of the bacterial classified sequences) than NF soils (11%). Pyrosequencing of the total 16S rRNA transcripts from microcosms at the whole community level further revealed hitherto unknown metabolisms of potential FER reduction by microorganisms including Pseudomonas and Solibacillus spp. in N soil, Dechloromonas, Clostridium, Bacillus and Solibacillus spp. in NF soil. Goethite (GOE) amendment stimulated Geobacter spp. to a lesser extent in both soils compared with FER treatment. Pseudomonas spp. in the N soil and Clostridium spp. in the NF soil may also be involved in GOE reduction. Pyrosequencing results from field samples showed that Geobacter spp. were the most abundant putative iron-reducers in both soils, and significantly stimulated by long-term nitrogen fertilization. Overall, for the first time, we demonstrate that long-term nitrogen fertilization promotes iron(III) reduction and modulates iron-reducing bacterial community in paddy soils. PMID:25171335

  13. CT-scout based, semi-automated vertebral morphometry after digital image enhancement.

    PubMed

    Glinkowski, Wojciech M; Narloch, Jerzy

    2017-09-01

    Radiographic diagnosis of osteoporotic vertebral fracture is necessary to reduce its substantial associated morbidity. Computed tomography (CT) scout has recently been demonstrated as a reliable technique for vertebral fracture diagnosis. Software assistance may help to overcome some limitations of that diagnostics. We aimed to evaluate whether digital image enhancement improved the capacity of one of the existing software to detect fractures semi-automatically. CT scanograms of patients suffering from osteoporosis, with or without vertebral fractures were analyzed. The original set of CT scanograms were triplicated and digitally modified to improve edge detection using three different techniques: SHARPENING, UNSHARP MASKING, and CONVOLUTION. The manual morphometric analysis identified 1485 vertebrae, 200 of which were classified as fractured. Unadjusted morphometry (AUTOMATED with no digital enhancement) found 63 fractures, 33 of which were true positive (i.e., it correctly identified 52% of the fractures); SHARPENING detected 57 fractures (30 true positives, 53%); UNSHARP MASKING yielded 30 (13 true positives, 43%); and CONVOLUTION found 24 fractures (9 true positives, 38%). The intra-reader reliability for height ratios did not significantly improve with image enhancement (kappa ranged 0.22-0.41 for adjusted measurements and 0.16-0.38 for unadjusted). Similarly, the inter-reader agreement for prevalent fractures did not significantly improve with image enhancement (kappa 0.29-0.56 and -0.01 to 0.23 for adjusted and unadjusted measurements, respectively). Our results suggest that digital image enhancement does not improve software-assisted vertebral fracture detection by CT scout. Copyright © 2017 Elsevier B.V. All rights reserved.

  14. Determination of the Relationship between Hydrologic Processes and Basin Morphometry - The Lamos Basin (Mersin, Turkey)

    NASA Astrophysics Data System (ADS)

    Yıldırım, Ümit; Güler, Cüneyt

    2016-04-01

    This study has been carried out to determine the relationship between hydrologic processes and basin morphometry in the Lamos Basin, which is located at the northern part of the Mersin (SE Turkey). The morphometric parameters of the basin was derived from the 1:25K scale topographic map sheets that were digitized using ArcGIS 9.3.1 geographic information system (GIS) software. Morphometric parameters considered in this study include basin area, basin length, basin perimeter length, stream order, stream number, stream length, mean stream length, basin relief, drainage density, stream frequency, drainage texture, bifurcation ratio, form factor, elongation ratio, overland flow length, relief ratio, and hypsometric integral. The results have shown that there are 1252 individual stream reaches with a total length of 1414.1 km in the Lamos basin, which covers an area of 1358 km2 and has a length of 103 km in the N-S direction. Furthermore, the basin has a medium drainage density of 1.04 1/km with a stream frequency and drainage texture values of 0.92 and 4.33, respectively. The basin can be classified as elongated because of the low values of elongation ratio (0.48) and form factor (0.12). The hypsometric integral of the basin (0.58) indicates that it is in the youth period and thus reasonably sensitive to erosion. The values of drainage texture, drainage density, and stream frequency indicate that the Lamos basin is moderately well drained, therefore overland flow in the basin is not expected to be so quick. Thus, in case of occurrence of sudden peak flows, sensitivity to the land sliding and erosion may increase further. As a result, it is suggested that human activities in the basin should be limited in areas in fairly close proximity to the present day stream network to prevent or reduce the risk to life and property.

  15. Comparative skeletal muscle fibre morphometry among wild birds with different locomotor behaviour

    PubMed Central

    TORRELLA, J. R.; FOUCES, V.; PALOMEQUE, J.; VISCOR, G.

    1998-01-01

    Six muscles of the mallard duck (Anas platyrhynchos), the common coot (Fulica atra) and the yellow-legged gull (Larus cachinnans) were analysed morphometrically, with special emphasis on their functional implications and physiological needs. Oxidative fibres always had significantly smaller size than anaerobic fibres, although no differences in the number of capillaries per fibre were found. This resulted in greater capillary counts per unit of fibre area and perimeter in oxidative than anaerobic fibres, which indicates that the greater demand for oxygen supply may be achieved by decreasing the size of the muscle fibre rather than by increasing the number of associated capillaries. Fast oxidative fibres of the pectoralis and the triceps of the gull had greater sizes than the fast oxidative fibres of the mallard and the coot, which correlates with the difference in energetic demands between flapping and gliding flight. Greater fibre cross-sectional areas and perimeters seem suited to afford the long-lasting activity with low metabolic demands required during gliding. By contrast, mallards and coots attain a high oxidative metabolism, during sustained flapping flight, by reducing fibre size at the expense of a diminished ability for force generation. Between-species comparisons of the hindlimb muscles only yielded differences for the anaerobic fibres of the gastrocnemius, as an important adaptive response to force generation during burst locomotion. The need to manage sustained swimming abilities effectively may result in similar FOG fibre morphometry of the hindlimb muscles studied, indicating that a compromise between the oxygen flux to the muscle cell and the development of power is highly optimised in oxidative fibres of the bird species studied. PMID:9643422

  16. Morphometry of impact craters on Mercury from MESSENGER altimetry and imaging

    NASA Astrophysics Data System (ADS)

    Susorney, Hannah C. M.; Barnouin, Olivier S.; Ernst, Carolyn M.; Johnson, Catherine L.

    2016-06-01

    Data acquired by the Mercury Laser Altimeter and the Mercury Dual Imaging System on the MESSENGER spacecraft in orbit about Mercury provide a means to measure the geometry of many of the impact craters in Mercury's northern hemisphere in detail for the first time. The combination of topographic and imaging data permit a systematic evaluation of impact crater morphometry on Mercury, a new calculation of the diameter Dt at which craters transition with increasing diameter from simple to complex forms, and an exploration of the role of target properties and impact velocity on final crater size and shape. Measurements of impact crater depth on Mercury confirm results from previous studies, with the exception that the depths of large complex craters are typically shallower at a given diameter than reported from Mariner 10 data. Secondary craters on Mercury are generally shallower than primary craters of the same diameter. No significant differences are observed between the depths of craters within heavily cratered terrain and those of craters within smooth plains. The morphological attributes of craters that reflect the transition from simple to complex craters do not appear at the same diameter; instead flat floors first appear with increasing diameter in craters at the smallest diameters, followed with increasing diameter by reduced crater depth and rim height, and then collapse and terracing of crater walls. Differences reported by others in Dt between Mercury and Mars (despite the similar surface gravitational acceleration on the two bodies) are confirmed in this study. The variations in Dt between Mercury and Mars cannot be adequately attributed to differences in either surface properties or mean projectile velocity.

  17. Computed Tomographic Morphometry of the Internal Anatomy of Mandibular Second Primary Molars.

    PubMed

    Kurthukoti, Ameet J; Sharma, Pranjal; Swamy, Dinesh Francis; Shashidara, R; Swamy, Elaine Barretto

    2015-01-01

    Need for the study: The most important procedure for a successful endodontic treatment is the cleaning and shaping of the canal system. Understanding the internal anatomy of teeth provides valuable information to the clinician that would help him achieve higher clinical success during endodontic therapy. To evaluate by computed tomography-the internal anatomy of mandibular second primary molars with respect to the number of canals, cross-sectional shape of canals, cross-sectional area of canals and the root dentin thickness. A total of 31 mandibular second primary molars were subjected to computed-tomographic evaluation in the transverse plane, after mounting them in a prefabricated template. The images, thus, obtained were analyzed using De-winter Bio-wizard® software. All the samples demonstrated two canals in the mesial root, while majority of the samples (65.48%) demonstrated two canals in the distal root. The cross-sectional images of the mesial canals demonstrated a round shape, while the distal canals demonstrated an irregular shape. The root dentin thickness was highly reduced on the distal aspect of mesial and mesial aspect of distal canals. The mandibular second primary molars demonstrated wide variation and complexities in their internal anatomy. A thorough understanding of the complexity of the root canal system is essential for understanding the principles and problems of shaping and cleaning, determining the apical limits and dimensions of canal preparations, and for performing successful endodontic procedures. How to cite this article: Kurthukoti AJ, Sharma P, Swamy DF, Shashidara R, Swamy EB. Computed Tomographic Morphometry of the Internal Anatomy of Mandibular Second Primary Molars. Int J Clin Pediatr Dent 2015;8(3):202-207.

  18. Longitudinal stability of MRI for mapping brain change using tensor-based morphometry

    PubMed Central

    Leow, Alex D.; Klunder, Andrea D.; Jack, Clifford R.; Toga, Arthur W.; Dale, Anders M.; Bernstein, Matt A.; Britson, Paula J.; Gunter, Jeffrey L.; Ward, Chadwick P.; Whitwell, Jennifer L.; Borowski, Bret J.; Fleisher, Adam S.; Fox, Nick C.; Harvey, Danielle; Kornak, John; Schuff, Norbert; Studholme, Colin; Alexander, Gene E.; Weiner, Michael W.; Thompson, Paul M.

    2007-01-01

    Measures of brain change can be computed from sequential MRI scans, providing valuable information on disease progression, e.g., for patient monitoring and drug trials. Tensor-based morphometry (TBM) creates maps of these brain changes, visualizing the 3D profile and rates of tissue growth or atrophy, but its sensitivity depends on the contrast and geometric stability of the images. A s part of the Alzheimer’s Disease Neuroimaging Initiative (ADNI), 17 normal elderly subjects were scanned twice (at a 2-week interval) with several 3D 1.5 T MRI pulse sequences: high and low flip angle SPGR/FLASH (from which Synthetic T1 images were generated), MP-RAGE, IR-SPGR (N = 10) and MEDIC (N = 7) scans. For each subject and scan type, a 3D deformation map aligned baseline and follow-up scans, computed with a nonlinear, inverse-consistent elastic registration algorithm. Voxelwise statistics, in ICBM stereotaxic space, visualized the profile of mean absolute change and its cross-subject variance; these maps were then compared using permutation testing. Image stability depended on: (1) the pulse sequence; (2) the transmit/receive coil type (birdcage versus phased array); (3) spatial distortion corrections (using MEDIC sequence information); (4) B1-field intensity inhomogeneity correction (using N3). SPGR/FLASH images acquired using a birdcage coil had least overall deviation. N3 correction reduced coil type and pulse sequence differences and improved scan reproducibility, except for Synthetic T1 images (which were intrinsically corrected for B1-inhomogeneity). No strong evidence favored B0 correction. Although SPGR/FLASH images showed least deviation here, pulse sequence selection for the ADNI project was based on multiple additional image analyses, to be reported elsewhere. PMID:16480900

  19. Morphometry and diffusion MR imaging years after childhood traumatic brain injury.

    PubMed

    Porto, Luciana; Jurcoane, Alina; Magerkurth, Joerg; Margerkurth, Joerg; Althaus, Jürgen; Zanella, Friedhelm; Hattingen, Elke; Kieslich, Matthias

    2011-11-01

    Our goal was to detect possible unrecognized injury in cerebral white matter (WM) in adult survivors of traumatic brain injury (TBI) during childhood, who showed no detectable axonal injury or chronic contusion on late conventional MRI. We used voxel-based morphometry (VBM) to detect subtle structural changes in brain morphology and diffusion-tensor imaging (DTI) to non-invasively probe WM integrity. By means of VBM and DTI we examined a group of 12 adult patients who suffered from childhood closed head injury without axonal injury on late conventional MRI. Patients sustained complicated mild or moderate-to-severe TBI with a mean of 7 points based on the Glasgow Coma Scale. The mean time after trauma was 19 years (range 7-31 years). For VBM, group comparisons of segmented T1-weighted grey matter and WM images were performed, while for DTI we compared the fractional anisotropy and mean diffusivity (MD) between the groups. Patients presented with higher MD in the right cerebral white matter, bilaterally in the forceps major and in the body and splenium of the corpus callosum. These findings were supported by VBM, which showed reduced WM volume bilaterally, mainly along the callosal splenium. Our results indicate that persistent focal long-term volume reduction and underlying WM structural changes may occur after TBI during childhood and that their effects extend into adulthood. Normal late conventional MR findings after childhood TBI do not rule out non-apparent axonal injury. Copyright © 2011 European Paediatric Neurology Society. Published by Elsevier Ltd. All rights reserved.

  20. Longitudinal stability of MRI for mapping brain change using tensor-based morphometry.

    PubMed

    Leow, Alex D; Klunder, Andrea D; Jack, Clifford R; Toga, Arthur W; Dale, Anders M; Bernstein, Matt A; Britson, Paula J; Gunter, Jeffrey L; Ward, Chadwick P; Whitwell, Jennifer L; Borowski, Bret J; Fleisher, Adam S; Fox, Nick C; Harvey, Danielle; Kornak, John; Schuff, Norbert; Studholme, Colin; Alexander, Gene E; Weiner, Michael W; Thompson, Paul M

    2006-06-01

    Measures of brain change can be computed from sequential MRI scans, providing valuable information on disease progression, e.g., for patient monitoring and drug trials. Tensor-based morphometry (TBM) creates maps of these brain changes, visualizing the 3D profile and rates of tissue growth or atrophy, but its sensitivity depends on the contrast and geometric stability of the images. As part of the Alzheimer's Disease Neuroimaging Initiative (ADNI), 17 normal elderly subjects were scanned twice (at a 2-week interval) with several 3D 1.5 T MRI pulse sequences: high and low flip angle SPGR/FLASH (from which Synthetic T1 images were generated), MP-RAGE, IR-SPGR (N = 10) and MEDIC (N = 7) scans. For each subject and scan type, a 3D deformation map aligned baseline and follow-up scans, computed with a nonlinear, inverse-consistent elastic registration algorithm. Voxelwise statistics, in ICBM stereotaxic space, visualized the profile of mean absolute change and its cross-subject variance; these maps were then compared using permutation testing. Image stability depended on: (1) the pulse sequence; (2) the transmit/receive coil type (birdcage versus phased array); (3) spatial distortion corrections (using MEDIC sequence information); (4) B1-field intensity inhomogeneity correction (using N3). SPGR/FLASH images acquired using a birdcage coil had least overall deviation. N3 correction reduced coil type and pulse sequence differences and improved scan reproducibility, except for Synthetic T1 images (which were intrinsically corrected for B1-inhomogeneity). No strong evidence favored B0 correction. Although SPGR/FLASH images showed least deviation here, pulse sequence selection for the ADNI project was based on multiple additional image analyses, to be reported elsewhere.

  1. STATISTICAL APPROACH TO BRAIN MORPHOMETRY DATA REQUIRED IN DEVELOPMENTAL NEUROTOXICITY (DNT) TESTING GUIDELINES: PROFILE ANALYSIS.

    EPA Science Inventory

    Brain morphometry measurements are required in test guidelines proposed by the USEPA to screen chemicals for developmental neurotoxicity. Because the DNT is a screening battery, the analysis of this data should be sensitive to dose-related changes in the pattern of brain growt...

  2. Annual Research Review: Progress in Using Brain Morphometry as a Clinical Tool for Diagnosing Psychiatric Disorders

    ERIC Educational Resources Information Center

    Haubold, Alexander; Peterson, Bradley S.; Bansal, Ravi

    2012-01-01

    Brain morphometry in recent decades has increased our understanding of the neural bases of psychiatric disorders by localizing anatomical disturbances to specific nuclei and subnuclei of the brain. At least some of these disturbances precede the overt expression of clinical symptoms and possibly are endophenotypes that could be used to diagnose an…

  3. Comparison of human sperm morphometry assessment models based on zona pellucida selectivity.

    PubMed

    Garrett, C; Liu, D Y; Baker, H W G

    2007-01-01

    Computer image analysis improves the objectivity and reproducibility of conventional assessments of sperm morphology. We have extended this objectivity by using the physiological process of sperm-zona pellucida (ZP) binding to classify 'normal' sperm morphometry. Linear regression analysis of the morphometric differences between sperm in semen, swim-up and ZP bound samples (n=53) was used to establish 12 "zona preferred" morphometric parameters from which two different morphometric evaluations of an individual sperm's potential for motility and ability to bind to the ZP of human oocytes were calculated. The two models, %Z and %ZB, were then tested, together with conventional morphometry assessments of percent "normal" and other semen variables, against experimental sperm-ZP binding rates (n=64) and natural pregnancy rates in sub-fertile couples (n= 1191). Although %ZB was the most significantly related semen variable to sperm-ZP binding rate, the simpler %Z was more significant in the Cox regression model for natural pregnancy rates in sub-fertile couples. In multivariate analysis, the only additional significant covariates were sperm straight line velocity and female age. %Z is therefore the most appropriate and also easiest of our morphometry assessments to be applied to commercial CASA systems which offer a morphometry module with stain density analysis.

  4. Neural Correlates of Communication Skill and Symptom Severity in Autism: A Voxel-Based Morphometry Study

    ERIC Educational Resources Information Center

    Parks, Lauren K.; Hill, Dina E.; Thoma, Robert J.; Euler, Matthew J.; Lewine, Jeffrey D.; Yeo, Ronald A.

    2009-01-01

    Although many studies have compared the brains of normal controls and individuals with autism, especially older, higher-functioning individuals with autism, little is known of the neural correlates of the vast clinical heterogeneity characteristic of the disorder. In this study, we used voxel-based morphometry (VBM) to examine gray matter…

  5. Annual Research Review: Progress in Using Brain Morphometry as a Clinical Tool for Diagnosing Psychiatric Disorders

    ERIC Educational Resources Information Center

    Haubold, Alexander; Peterson, Bradley S.; Bansal, Ravi

    2012-01-01

    Brain morphometry in recent decades has increased our understanding of the neural bases of psychiatric disorders by localizing anatomical disturbances to specific nuclei and subnuclei of the brain. At least some of these disturbances precede the overt expression of clinical symptoms and possibly are endophenotypes that could be used to diagnose an…

  6. Supremacy of modern morphometry in typing renal oncocytoma and malignant look-alikes.

    PubMed

    Erlmeier, Franziska; Feuchtinger, Annette; Borgmann, Daniela; Rudelius, Martina; Autenrieth, Michael; Walch, Axel Karl; Weirich, Gregor

    2015-08-01

    In the era of tumour type-specific therapies, the correct typing of renal tumours is of prime importance. As immunotyping and genotyping approaches are laborious and fall short of standardization, we used whole-scale computer-assisted morphometry instead. Three different types of renal tumours with different prognoses and therapies, notoriously prone to mistyping, were analysed . The sample of 335 tumours included clear cell renal cell carcinoma, chromophobe renal cell carcinoma and renal oncocytoma. The sample was analysed using H&E stains of tissue microarrrays in combination with an image-scanning software. Nuclear and cytoplasmic features were registered with the aid of computer-assisted morphometry. Features included shape, texture, colour and colour intensity for different cell compartments, e.g. nuclei and cytoplasm. The software passed several training steps for final validation. Using morphometry, we were able to classify the three renal tumour types correctly, with a 100 % specificity compared to the WHO typing. Nuclear features dominated the typing of chromophobe renal cell carcinoma, whereas cytoplasmic features were the leading classificators for renal oncocytoma. The grading of clear cell renal cell carcinoma attained a specificity of 80 %. In conclusion, modern morphometry may serve as a tool for typing renal epithelial tumours and additionally draws the attention to future nuclear research in chromophobe renal cell carcinoma.

  7. Yeast population dynamics reveal a potential 'collaboration' between Metschnikowia pulcherrima and Saccharomyces uvarum for the production of reduced alcohol wines during Shiraz fermentation.

    PubMed

    Contreras, A; Curtin, C; Varela, C

    2015-02-01

    The wine sector is actively seeking strategies and technologies that facilitate the production of wines with lower alcohol content. One of the simplest approaches to achieve this aim would be the use of wine yeast strains which are less efficient at transforming grape sugars into ethanol; however, commercial wine yeasts have very similar ethanol yields. We recently demonstrated that Metschnikowia pulcherrima AWRI1149 was able to produce wine with reduced alcohol concentration when used in sequential inoculation with a wine strain of Saccharomyces cerevisiae. Here, different inoculation regimes were explored to study the effect of yeast population dynamics and potential yeast interactions on the metabolism of M. pulcherrima AWRI1149 during fermentation of non-sterile Shiraz must. Of all inoculation regimes tested, only ferments inoculated with M. pulcherrima AWRI1149 showed reduced ethanol concentration. Population dynamics revealed the presence of several indigenous yeast species and one of these, Saccharomyces uvarum (AWRI 2846), was able to produce wine with reduced ethanol concentration in sterile conditions. Both strains however, were inhibited when a combination of three non-Saccharomyces strains, Hanseniaspora uvarum AWRI863, Pichia kluyveri AWRI1896 and Torulaspora delbrueckii AWRI2845 were inoculated into must, indicating that the microbial community composition might impact on the growth of M. pulcherrima AWRI1149 and S. uvarum AWRI 2846. Our results indicate that mixed cultures of M. pulcherrima AWRI1149 and S. uvarum AWRI2846 enable an additional reduction of wine ethanol concentration compared to the same must fermented with either strain alone. This work thus provides a foundation to develop inoculation regimes for the successful application of non-cerevisiae yeast to the production of wines with reduced alcohol.

  8. Comparative analysis of single and combined APP/APLP knockouts reveals reduced spine density in APP-KO mice that is prevented by APPsα expression

    PubMed Central

    2014-01-01

    Synaptic dysfunction and synapse loss are key features of Alzheimer’s pathogenesis. Previously, we showed an essential function of APP and APLP2 for synaptic plasticity, learning and memory. Here, we used organotypic hippocampal cultures to investigate the specific role(s) of APP family members and their fragments for dendritic complexity and spine formation of principal neurons within the hippocampus. Whereas CA1 neurons from APLP1-KO or APLP2-KO mice showed normal neuronal morphology and spine density, APP-KO mice revealed a highly reduced dendritic complexity in mid-apical dendrites. Despite unaltered morphology of APLP2-KO neurons, combined APP/APLP2-DKO mutants showed an additional branching defect in proximal apical dendrites, indicating redundancy and a combined function of APP and APLP2 for dendritic architecture. Remarkably, APP-KO neurons showed a pronounced decrease in spine density and reductions in the number of mushroom spines. No further decrease in spine density, however, was detectable in APP/APLP2-DKO mice. Mechanistically, using APPsα-KI mice lacking transmembrane APP and expressing solely the secreted APPsα fragment we demonstrate that APPsα expression alone is sufficient to prevent the defects in spine density observed in APP-KO mice. Collectively, these studies reveal a combined role of APP and APLP2 for dendritic architecture and a unique function of secreted APPs for spine density. PMID:24684730

  9. Urinary loss of tricarboxylic acid cycle intermediates as revealed by metabolomics studies: an underlying mechanism to reduce lipid accretion by whey protein ingestion?

    PubMed

    Lillefosse, Haldis H; Clausen, Morten R; Yde, Christian C; Ditlev, Ditte B; Zhang, Xumin; Du, Zhen-Yu; Bertram, Hanne C; Madsen, Lise; Kristiansen, Karsten; Liaset, Bjørn

    2014-05-02

    Whey protein intake is associated with the modulation of energy metabolism and altered body composition both in human subjects and in animals, but the underlying mechanisms are not yet elucidated. We fed obesity-prone C57BL/6J mice high-fat diets with either casein (HF casein) or whey (HF whey) for 6 weeks. At equal energy intake and apparent fat and nitrogen digestibility, mice fed HF whey stored less energy as lipids, evident both as lower white adipose tissue mass and as reduced liver lipids, compared with HF-casein-fed mice. Explorative analyses of 48 h urine, both by (1)H NMR and LC-MS metabolomic platforms, demonstrated higher urinary excretion of tricarboxylic acid (TCA) cycle intermediates citric acid and succinic acid (identified by both platforms), and cis-aconitic acid and isocitric acid (identified by LC-MS platform) in the HF whey, relative to in the HF-casein-fed mice. Targeted LC-MS analyses revealed higher citric acid and cis-aconitic acid concentrations in fed state plasma, but not in liver of HF-whey-fed mice. We propose that enhanced urinary loss of TCA cycle metabolites drain available substrates for anabolic processes, such as lipogenesis, thereby leading to reduced lipid accretion in HF-whey-fed compared to HF-casein-fed mice.

  10. Genome-wide transcriptomic analysis reveals correlation between higher WRKY61 expression and reduced symptom severity in Turnip crinkle virus infected Arabidopsis thaliana

    PubMed Central

    Gao, Ruimin; Liu, Peng; Yong, Yuhan; Wong, Sek-Man

    2016-01-01

    Turnip crinkle virus (TCV) is a carmovirus that infects many Arabidopsis ecotypes. Most studies mainly focused on discovery of resistance genes against TCV infection, and there is no Next Generation Sequencing based comparative genome wide transcriptome analysis reported. In this study, RNA-seq based transcriptome analysis revealed that 238 (155 up-regulated and 83 down-regulated) significant differentially expressed genes with at least 15-fold change were determined. Fifteen genes (including upregulated, unchanged and downregulated) were selected for RNA-seq data validation using quantitative real-time PCR, which showed consistencies between these two sets of data. GO enrichment analysis showed that numerous terms such as stress, immunity, defence and chemical stimulus were affected in TCV-infected plants. One putative plant defence related gene named WRKY61 was selected for further investigation. It showed that WRKY61 overexpression plants displayed reduced symptoms and less virus accumulation, as compared to wild type (WT) and WRKY61 deficient lines, suggesting that higher WRKY61 expression level reduced TCV viral accumulation. In conclusion, our transcriptome analysis showed that global gene expression was detected in TCV-infected Arabidopsis thaliana. WRKY61 gene was shown to be negatively correlated with TCV infection and viral symptoms, which may be connected to plant immunity pathways. PMID:27086702

  11. Urinary Loss of Tricarboxylic Acid Cycle Intermediates As Revealed by Metabolomics Studies: An Underlying Mechanism to Reduce Lipid Accretion by Whey Protein Ingestion?

    PubMed Central

    2015-01-01

    Whey protein intake is associated with the modulation of energy metabolism and altered body composition both in human subjects and in animals, but the underlying mechanisms are not yet elucidated. We fed obesity-prone C57BL/6J mice high-fat diets with either casein (HF casein) or whey (HF whey) for 6 weeks. At equal energy intake and apparent fat and nitrogen digestibility, mice fed HF whey stored less energy as lipids, evident both as lower white adipose tissue mass and as reduced liver lipids, compared with HF-casein-fed mice. Explorative analyses of 48 h urine, both by 1H NMR and LC–MS metabolomic platforms, demonstrated higher urinary excretion of tricarboxylic acid (TCA) cycle intermediates citric acid and succinic acid (identified by both platforms), and cis-aconitic acid and isocitric acid (identified by LC–MS platform) in the HF whey, relative to in the HF-casein-fed mice. Targeted LC–MS analyses revealed higher citric acid and cis-aconitic acid concentrations in fed state plasma, but not in liver of HF-whey-fed mice. We propose that enhanced urinary loss of TCA cycle metabolites drain available substrates for anabolic processes, such as lipogenesis, thereby leading to reduced lipid accretion in HF-whey-fed compared to HF-casein-fed mice. PMID:24702026

  12. Microarray and Functional Gene Analyses of Sulfate-Reducing Prokaryotes in Low-Sulfate, Acidic Fens Reveal Cooccurrence of Recognized Genera and Novel Lineages

    PubMed Central

    Loy, Alexander; Küsel, Kirsten; Lehner, Angelika; Drake, Harold L.; Wagner, Michael

    2004-01-01

    Low-sulfate, acidic (approximately pH 4) fens in the Lehstenbach catchment in the Fichtelgebirge mountains in Germany are unusual habitats for sulfate-reducing prokaryotes (SRPs) that have been postulated to facilitate the retention of sulfur and protons in these ecosystems. Despite the low in situ availability of sulfate (concentration in the soil solution, 20 to 200 μM) and the acidic conditions (soil and soil solution pHs, approximately 4 and 5, respectively), the upper peat layers of the soils from two fens (Schlöppnerbrunnen I and II) of this catchment displayed significant sulfate-reducing capacities. 16S rRNA gene-based oligonucleotide microarray analyses revealed stable diversity patterns for recognized SRPs in the upper 30 cm of both fens. Members of the family “Syntrophobacteraceae” were detected in both fens, while signals specific for the genus Desulfomonile were observed only in soils from Schlöppnerbrunnen I. These results were confirmed and extended by comparative analyses of environmentally retrieved 16S rRNA and dissimilatory (bi)sulfite reductase (dsrAB) gene sequences; dsrAB sequences from Desulfobacca-like SRPs, which were not identified by microarray analysis, were obtained from both fens. Hypotheses concerning the ecophysiological role of these three SRP groups in the fens were formulated based on the known physiological properties of their cultured relatives. In addition to these recognized SRP lineages, six novel dsrAB types that were phylogenetically unrelated to all known SRPs were detected in the fens. These dsrAB sequences had no features indicative of pseudogenes and likely represent novel, deeply branching, sulfate- or sulfite-reducing prokaryotes that are specialized colonists of low-sulfate habitats. PMID:15574893

  13. Nuclear resonance vibrational spectroscopy reveals the FeS cluster composition and active site vibrational properties of an O2-tolerant NAD+-reducing [NiFe] hydrogenase

    DOE PAGES

    Lauterbach, Lars; Wang, Hongxin; Horch, Marius; ...

    2014-10-30

    Hydrogenases are complex metalloenzymes that catalyze the reversible splitting of molecular hydrogen into protons and electrons essentially without overpotential. The NAD+-reducing soluble hydrogenase (SH) from Ralstonia eutropha is capable of H2 conversion even in the presence of usually toxic dioxygen. The molecular details of the underlying reactions are largely unknown, mainly because of limited knowledge of the structure and function of the various metal cofactors present in the enzyme. Here, all iron-containing cofactors of the SH were investigated by 57Fe specific nuclear resonance vibrational spectroscopy (NRVS). Our data provide experimental evidence for one [2Fe2S] center and four [4Fe4S] clusters, whichmore » is consistent with the amino acid sequence composition. Only the [2Fe2S] cluster and one of the four [4Fe4S] clusters were reduced upon incubation of the SH with NADH. This finding explains the discrepancy between the large number of FeS clusters and the small amount of FeS cluster-related signals as detected by electron paramagnetic resonance spectroscopic analysis of several NAD+-reducing hydrogenases. For the first time, Fe–CO and Fe–CN modes derived from the [NiFe] active site could be distinguished by NRVS through selective 13C labeling of the CO ligand. This strategy also revealed the molecular coordinates that dominate the individual Fe–CO modes. The present approach explores the complex vibrational signature of the Fe–S clusters and the hydrogenase active site, thereby showing that NRVS represents a powerful tool for the elucidation of complex biocatalysts containing multiple cofactors.« less

  14. Effect of zinc on growth performance, gut morphometry, and cecal microbial community in broilers challenged with Salmonella enterica serovar typhimurium.

    PubMed

    Shao, Yuxin; Lei, Zhao; Yuan, Jianmin; Yang, Ying; Guo, Yuming; Zhang, Bingkun

    2014-12-01

    To evaluate the effects of supplemental zinc on growth performance, gut morphometry, and the cecal microbial community in broilers challenged with Salmonella typhimurium, 180, 1-day-old male Cobb 500 broiler chicks were randomly assigned to 3 treatments with ten replicates for a 42 day experiment. The 3 treatments were: unchallenged, S. typhimurium-challenged, and S. typhimurium-challenged with 120 mg/kg of zinc supplementation in the diet. Salmonella infection caused a reduction in body-weight gain and feed intake, disrupted the intestinal structure by decreasing the villus-height/crypt-depth ratio of the ileum and increasing the apoptotic index of ileal epithelial cells. Moreover, the cecal microbial community was altered by Salmonella infection, as demonstrated by a reduced number of Lactobacillus and total bacteria. Dietary zinc supplementation improved growth performance by increasing the body-weight gain and feed intake in the challenged broilers. In addition, zinc repaired intestinal injury by reducing the apoptotic index of ileal epithelial cells, enhancing villus height and the villus-height/crypt-depth ratio of the ileum, and the proliferation index of ileal epithelial cells. Finally, zinc regulated the cecal microbial community by increasing the number of total bacteria and beneficial Lactobacillus bacteria, and reducing the number of Salmonella. The results indicated that dietary zinc supplementation improved growth performance, intestinal morphology, and intestinal microbiota in S. typhimurium-challenged broilers.

  15. Surface-based vertexwise analysis of morphometry and microstructural integrity for white matter tracts in diffusion tensor imaging: With application to the corpus callosum in Alzheimer's disease.

    PubMed

    Tang, Xiaoying; Qin, Yuanyuan; Zhu, Wenzhen; Miller, Michael I

    2017-04-01

    In this article, we present a unified statistical pipeline for analyzing the white matter (WM) tracts morphometry and microstructural integrity, both globally and locally within the same WM tract, from diffusion tensor imaging. Morphometry is quantified globally by the volumetric measurement and locally by the vertexwise surface areas. Meanwhile, microstructural integrity is quantified globally by the mean fractional anisotropy (FA) and trace values within the specific WM tract and locally by the FA and trace values defined at each vertex of its bounding surface. The proposed pipeline consists of four steps: (1) fully automated segmentation of WM tracts in a multi-contrast multi-atlas framework; (2) generation of the smooth surface representations for the WM tracts of interest; (3) common template surface generation on which the localized morphometric and microstructural statistics are defined and a variety of statistical analyses can be conducted; (4) multiple comparison correction to determine the significance of the statistical analysis results. Detailed herein, this pipeline has been applied to the corpus callosum in Alzheimer's disease (AD) with significantly decreased FA values and increased trace values, both globally and locally, being detected in patients with AD when compared to normal aging populations. A subdivision of the corpus callosum in both hemispheres revealed that the AD pathology primarily affects the body and splenium of the corpus callosum. Validation analyses and two multiple comparison correction strategies are provided. Hum Brain Mapp 38:1875-1893, 2017. © 2017 Wiley Periodicals, Inc.

  16. Analyses of Rock Size-Frequency Distributions and Morphometry of Modified Hawaiian Lava Flows: Implications for Future Martian Landing Sites

    NASA Technical Reports Server (NTRS)

    Craddock, Robert A.; Golombek, Matthew; Howard, Alan D.

    2000-01-01

    Both the size-frequency distribution and morphometry of rock populations emplaced by a variety of geologic processes in Hawaii indicate that such information may be useful in planning future landing sites on Mars and interpreting the surface geology.

  17. Single molecule analysis of a red fluorescent RecA protein reveals a defect in nucleoprotein filament nucleation that relates to its reduced biological functions.

    PubMed

    Handa, Naofumi; Amitani, Ichiro; Gumlaw, Nathan; Sandler, Steven J; Kowalczykowski, Stephen C

    2009-07-10

    Fluorescent fusion proteins are exceedingly useful for monitoring protein localization in situ or visualizing protein behavior at the single molecule level. Unfortunately, some proteins are rendered inactive by the fusion. To circumvent this problem, we fused a hyperactive RecA protein (RecA803 protein) to monomeric red fluorescent protein (mRFP1) to produce a functional protein (RecA-RFP) that is suitable for in vivo and in vitro analysis. In vivo, the RecA-RFP partially restores UV resistance, conjugational recombination, and SOS induction to recA(-) cells. In vitro, the purified RecA-RFP protein forms a nucleoprotein filament whose k(cat) for single-stranded DNA-dependent ATPase activity is reduced approximately 3-fold relative to wild-type protein, and which is largely inhibited by single-stranded DNA-binding protein. However, RecA protein is also a dATPase; dATP supports RecA-RFP nucleoprotein filament formation in the presence of single-stranded DNA-binding protein. Furthermore, as for the wild-type protein, the activities of RecA-RFP are further enhanced by shifting the pH to 6.2. As a consequence, RecA-RFP is proficient for DNA strand exchange with dATP or at lower pH. Finally, using single molecule visualization, RecA-RFP was seen to assemble into a continuous filament on duplex DNA, and to extend the DNA approximately 1.7-fold. Consistent with its attenuated activities, RecA-RFP nucleates onto double-stranded DNA approximately 3-fold more slowly than the wild-type protein, but still requires approximately 3 monomers to form the rate-limited nucleus needed for filament assembly. Thus, RecA-RFP reveals that its attenuated biological functions correlate with a reduced frequency of nucleoprotein filament nucleation at the single molecule level.

  18. Chemically induced conditional rescue of the reduced epidermal fluorescence8 mutant of Arabidopsis reveals rapid restoration of growth and selective turnover of secondary metabolite pools.

    PubMed

    Kim, Jeong Im; Ciesielski, Peter N; Donohoe, Bryon S; Chapple, Clint; Li, Xu

    2014-02-01

    The phenylpropanoid pathway is responsible for the biosynthesis of diverse and important secondary metabolites including lignin and flavonoids. The reduced epidermal fluorescence8 (ref8) mutant of Arabidopsis (Arabidopsis thaliana), which is defective in a lignin biosynthetic enzyme p-coumaroyl shikimate 3'-hydroxylase (C3'H), exhibits severe dwarfism and sterility. To better understand the impact of perturbation of phenylpropanoid metabolism on plant growth, we generated a chemically inducible C3'H expression construct and transformed it into the ref8 mutant. Application of dexamethasone to these plants greatly alleviates the dwarfism and sterility and substantially reverses the biochemical phenotypes of ref8 plants, including the reduction of lignin content and hyperaccumulation of flavonoids and p-coumarate esters. Induction of C3'H expression at different developmental stages has distinct impacts on plant growth. Although early induction effectively restored the elongation of primary inflorescence stem, application to 7-week-old plants enabled them to produce new rosette inflorescence stems. Examination of hypocotyls of these plants revealed normal vasculature in the newly formed secondary xylem, presumably restoring water transport in the mutant. The ref8 mutant accumulates higher levels of salicylic acid than the wild type, but depletion of this compound in ref8 did not relieve the mutant's growth defects, suggesting that the hyperaccumulation of salicylic acid is unlikely to be responsible for dwarfism in this mutant.

  19. Crystal Structure of Reduced and of Oxidized Peroxiredoxin IV Enzyme Reveals a Stable Oxidized Decamer and a Non-disulfide-bonded Intermediate in the Catalytic Cycle*

    PubMed Central

    Cao, Zhenbo; Tavender, Timothy J.; Roszak, Aleksander W.; Cogdell, Richard J.; Bulleid, Neil J.

    2011-01-01

    Peroxiredoxin IV (PrxIV) is an endoplasmic reticulum-localized enzyme that metabolizes the hydrogen peroxide produced by endoplasmic reticulum oxidase 1 (Ero1). It has been shown to play a role in de novo disulfide formation, oxidizing members of the protein disulfide isomerase family of enzymes, and is a member of the typical 2-Cys peroxiredoxin family. We have determined the crystal structure of both reduced and disulfide-bonded, as well as a resolving cysteine mutant of human PrxIV. We show that PrxIV has a similar structure to other typical 2-Cys peroxiredoxins and undergoes a conformational change from a fully folded to a locally unfolded form following the formation of a disulfide between the peroxidatic and resolving cysteine residues. Unlike other mammalian typical 2-Cys peroxiredoxins, we show that human PrxIV forms a stable decameric structure even in its disulfide-bonded state. In addition, the structure of a resolving cysteine mutant reveals an intermediate in the reaction cycle that adopts the locally unfolded conformation. Interestingly the peroxidatic cysteine in the crystal structure is sulfenylated rather than sulfinylated or sulfonylated. In addition, the peroxidatic cysteine in the resolving cysteine mutant is resistant to hyper-oxidation following incubation with high concentrations of hydrogen peroxide. These results highlight some unique properties of PrxIV and suggest that the equilibrium between the fully folded and locally unfolded forms favors the locally unfolded conformation upon sulfenylation of the peroxidatic cysteine residue. PMID:21994946

  20. Brain morphometric biomarkers distinguishing unipolar and bipolar depression. A voxel-based morphometry-pattern classification approach.

    PubMed

    Redlich, Ronny; Almeida, Jorge J R; Grotegerd, Dominik; Opel, Nils; Kugel, Harald; Heindel, Walter; Arolt, Volker; Phillips, Mary L; Dannlowski, Udo

    2014-11-01

    The structural abnormalities in the brain that accurately differentiate unipolar depression (UD) and bipolar depression (BD) remain unidentified. First, to investigate and compare morphometric changes in UD and BD, and to replicate the findings at 2 independent neuroimaging sites; second, to differentiate UD and BD using multivariate pattern classification techniques. In a 2-center cross-sectional study, structural gray matter data were obtained at 2 independent sites (Pittsburgh, Pennsylvania, and Münster, Germany) using 3-T magnetic resonance imaging. Voxel-based morphometry was used to compare local gray and white matter volumes, and a novel pattern classification approach was used to discriminate between UD and BD, while training the classifier at one imaging site and testing in an independent sample at the other site. The Pittsburgh sample of participants was recruited from the Western Psychiatric Institute and Clinic at the University of Pittsburgh from 2008 to 2012. The Münster sample was recruited from the Department of Psychiatry at the University of Münster from 2010 to 2012. Equally divided between the 2 sites were 58 currently depressed patients with bipolar I disorder, 58 age- and sex-matched unipolar depressed patients, and 58 matched healthy controls. Magnetic resonance imaging was used to detect structural differences between groups. Morphometric analyses were applied using voxel-based morphometry. Pattern classification techniques were used for a multivariate approach. At both sites, individuals with BD showed reduced gray matter volumes in the hippocampal formation and the amygdala relative to individuals with UD (Montreal Neurological Institute coordinates x = -22, y = -1, z = 20; k = 1938 voxels; t = 4.75), whereas individuals with UD showed reduced gray matter volumes in the anterior cingulate gyrus compared with individuals with BD (Montreal Neurological Institute coordinates x = -8, y = 32, z = 3; k

  1. The geomorphology and morphometry of the banded terrain in Hellas basin, Mars

    NASA Astrophysics Data System (ADS)

    Diot, X.; El-Maarry, M. R.; Schlunegger, F.; Norton, K. P.; Thomas, N.; Grindrod, P. M.

    2014-10-01

    Hellas basin is a large impact basin situated in the southern highlands of Mars. The north-western part of the basin has the lowest elevation (-7.5 km) on the planet and contains a possibly unique terrain type, which we informally call “banded terrain”. The banded terrain is made up of smooth-looking banded deposits that display signs of viscous behavior and a paucity of superimposed impact craters. In this study, we use newly acquired high spatial resolution images from the High Resolution Imaging Science Experiment (HiRISE) in addition to existing datasets to characterize the geomorphology, the morphometry and the architecture of the banded terrain. The banded terrain is generally confined to the NW edge of the Alpheus Colles plateau. The individual bands are ~3-15 km-long, ~0.3 km-wide and are separated by narrow inter-band depressions, which are ~65 m-wide and ~10 m-deep. The bands display several morphologies that vary from linear to concentric forms. Morphometric analysis reveals that the slopes along a given linear or lobate band ranges from 0.5° to 15° (average ~6°), whereas the concentric bands are located on flatter terrain (average slope ~2-3°). Crater-size frequency analysis yields an Amazonian-Hesperian boundary crater retention age for the terrain (~3 Gyr), which together, with the presence of very few degraded craters, either implies a recent emplacement, resurfacing, or intense erosion. The apparent sensitivity to local topography and preference for concentrating in localized depressions is compatible with deformation as a viscous fluid. In addition, the bands display clear signs of degradation and slumping at their margins along with a suite of other features that include fractured mounds, polygonal cracks at variable size-scales, and knobby/hummocky textures. Together, these features suggest an ice-rich composition for at least the upper layers of the terrain, which is currently being heavily modified through loss of ice and intense

  2. Grey matter changes associated with deficit awareness in mild cognitive impairment: a voxel-based morphometry study.

    PubMed

    Ford, Andrew H; Almeida, Osvaldo P; Flicker, Leon; Garrido, Griselda J; Greenop, Kathryn R; Foster, Jonathan K; Etherton-Beer, Christopher; van Bockxmeer, Frank M; Lautenschlager, Nicola T

    2014-01-01

    Reduced awareness of cognitive deficits in mild cognitive impairment (MCI) is associated with poorer outcomes although little is known about the anatomical correlates of this. We examined the association of insight and grey matter volume using a voxel-based morphometry approach in 65 volunteers with MCI and 55 healthy age-matched controls. Participants with MCI had multiple areas of subtle grey matter volume loss compared with controls, although these did not survive correction for multiple comparisons. These were predominantly in the temporal and anterior portions of the brain. Individuals with MCI did not differ from each other on a number of demographic and cognitive variables according to level of insight. Reduced awareness of cognitive deficits was associated with few differences in grey matter volume apart from a subtle loss of grey matter in the medial frontal gyri. Given the modest nature of these findings, the routine assessment of insight in non-clinical populations of individuals with MCI is therefore not supported. Prospective data in larger samples, however, would be helpful to clarify this further and determine if impaired insight predicts brain atrophy and cognitive decline.

  3. Effects of intra-uterine and early extra-uterine malnutrition on seizure threshold and hippocampal morphometry of pup rats.

    PubMed

    Florian, Mariana Lorenzet; Nunes, Magda Lahorgue

    2010-12-01

    We evaluate the influence of different malnutrition paradigms (intra-uterine × extra-uterine) in body and brain weight, in seizure threshold and in hippocampus morphometry, in developing rats. Intra-uterine malnutrition model consisted in reduction by half of the ration offered to pregnant female; extra-uterine malnutrition consisted of progressive limitation of lactation, from P2 to P15. Seizure induction was accomplished by exposure to flurothyl, at P15. At the same day animals were sacrificed. Morphometric analysis was based on hippocampal pyramidal and granular cells estimate number, through volume calculation and cellular density. Extra-uterine malnutrition significantly reduced pups body and brain weight, seizure threshold and neuronal number in CA4 region only. Intra-uterine malnutrition reduced neuronal number in CA2, CA4 and DG regions regarding well-nourished and extra-uterine malnourished animals. In CA3, CA4 and dentate gyrus, a significant cell increase was observed in groups exposed to seizures, regarding similar control groups.

  4. Effects of intra-uterine and early extra-uterine malnutrition on seizure threshold and hippocampal morphometry of pup rats.

    PubMed

    Florian, Mariana Lorenzet; Nunes, Magda Lahorgue

    2011-07-01

    We evaluate the influence of different malnutrition paradigms (intra-uterine x extra-uterine) in body and brain weight, in seizure threshold and in hippocampus morphometry, in developing rats. Intra-uterine malnutrition model consisted in reduction by half of the ration offered to pregnant female; extrauterine malnutrition consisted of progressive limitation of lactation, from P2 to P15. Seizure induction was accomplished by exposure to flurothyl, at P15. At the same day animals were sacrificed. Morphometric analysis was based on hippocampal pyramidal and granular cells estimate number, through volume calculation and cellular density. Extra-uterine malnutrition significantly reduced pups body and brain weight, seizure threshold and neuronal number in CA4 region only. Intra-uterine malnutrition reduced neuronal number in CA2, CA4 and DG regions regarding well-nourished and extra-uterine malnourished animals. In CA3, CA4 and dentate gyrus, a significant cell increase was observed in groups exposed to seizures, regarding similar control groups.

  5. Effect of cocaine on structural changes in brain: MRI volumetry using tensor-based morphometry.

    PubMed

    Narayana, Ponnada A; Datta, Sushmita; Tao, Guozhi; Steinberg, Joel L; Moeller, F Gerard

    2010-10-01

    Magnetic resonance imaging (MRI) was performed in cocaine-dependent subjects to determine the structural changes in brain compared to non-drug using controls. Cocaine-dependent subjects and controls were carefully screened to rule out brain pathology of undetermined origin. Magnetic resonance images were analyzed using tensor-based morphometry (TBM) and voxel-based morphometry (VBM) without and with modulation to adjust for volume changes during normalization. For TBM analysis, unbiased atlases were generated using two different inverse consistent and diffeomorphic nonlinear registration techniques. Two different control groups were used for generating unbiased atlases. Independent of the nonlinear registration technique and normal cohorts used for creating the unbiased atlases, our analysis failed to detect any statistically significant effect of cocaine on brain volumes. These results show that cocaine-dependent subjects do not show differences in regional brain volumes compared to non-drug using controls. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

  6. Morphometry and average temperature affect lake stratification responses to climate change

    NASA Astrophysics Data System (ADS)

    Kraemer, Benjamin M.; Anneville, Orlane; Chandra, Sudeep; Dix, Margaret; Kuusisto, Esko; Livingstone, David M.; Rimmer, Alon; Schladow, S. Geoffrey; Silow, Eugene; Sitoki, Lewis M.; Tamatamah, Rashid; Vadeboncoeur, Yvonne; McIntyre, Peter B.

    2015-06-01

    Climate change is affecting lake stratification with consequences for water quality and the benefits that lakes provide to society. Here we use long-term temperature data (1970-2010) from 26 lakes around the world to show that climate change has altered lake stratification globally and that the magnitudes of lake stratification changes are primarily controlled by lake morphometry (mean depth, surface area, and volume) and mean lake temperature. Deep lakes and lakes with high average temperatures have experienced the largest changes in lake stratification even though their surface temperatures tend to be warming more slowly. These results confirm that the nonlinear relationship between water density and water temperature and the strong dependence of lake stratification on lake morphometry makes lake temperature trends relatively poor predictors of lake stratification trends.

  7. A reexamination of age-related variation in body weight and morphometry of Maryland nutria

    USGS Publications Warehouse

    Sherfy, M.H.; Mollett, T.A.; McGowan, K.R.; Daugherty, S.L.

    2006-01-01

    Age-related variation in morphometry has been documented for many species. Knowledge of growth patterns can be useful for modeling energetics, detecting physiological influences on populations, and predicting age. These benefits have shown value in understanding population dynamics of invasive species, particularly in developing efficient control and eradication programs. However, development and evaluation of descriptive and predictive models is a critical initial step in this process. Accordingly, we used data from necropsies of 1,544 nutria (Myocastor coypus) collected in Maryland, USA, to evaluate the accuracy of previously published models for prediction of nutria age from body weight. Published models underestimated body weights of our animals, especially for ages <3. We used cross-validation procedures to develop and evaluate models for describing nutria growth patterns and for predicting nutria age. We derived models from a randomly selected model-building data set (n = 192-193 M, 217-222 F) and evaluated them with the remaining animals (n = 487-488 M, 642-647 F). We used nonlinear regression to develop Gompertz growth-curve models relating morphometric variables to age. Predicted values of morphometric variables fell within the 95% confidence limits of their true values for most age classes. We also developed predictive models for estimating nutria age from morphometry, using linear regression of log-transformed age on morphometric variables. The evaluation data set corresponded with 95% prediction intervals from the new models. Predictive models for body weight and length provided greater accuracy and less bias than models for foot length and axillary girth. Our growth models accurately described age-related variation in nutria morphometry, and our predictive models provided accurate estimates of ages from morphometry that will be useful for live-captured individuals. Our models offer better accuracy and precision than previously published models

  8. A review of recent developments and applications of morphometry/stereology in lung research.

    PubMed

    Mühlfeld, Christian; Hegermann, Jan; Wrede, Christoph; Ochs, Matthias

    2015-09-15

    Design-based stereology is the gold standard of morphometry in lung research. Here, we analyze the current use of morphometric and stereological methods in lung research and provide an overview on recent methodological developments and biological observations made by the use of stereology. Based on this analysis we hope to provide useful recommendations for a good stereological practice to further the use of advanced and unbiased stereological methods.

  9. Amygdala Atrophy in MCI/Alzheimer's Disease in the BIOCARD cohort based on Diffeomorphic Morphometry.

    PubMed

    Miller, Michael I; Younes, Laurent; Ratnanather, J Tilak; Brown, Timothy; Reigel, Tommy; Trinh, Huong; Tang, Xiaoying; Barker, Peter; Mori, Susumu; Albert, Marilyn

    2012-10-01

    Surface-based deformation markers obtained from diffeomorphic mapping of the amygdala are used to study specific atrophy patterns in a combined mild cognitively impaired and demented cohort compared with cognitively normal aging subjects. Statistical analysis demonstrates with high significance in a small sample of legacy data that deformation-based morphometry provides sensitive markers for locating atrophy in the amygdala. With respect to a high-field amygdala atlas, significant atrophy was found in the basomedial and lateral nucleus subregions.

  10. Influence of Group on Individual Subject Maps in SPM Voxel Based Morphometry

    PubMed Central

    Michael, Andrew M.; Evans, Eli; Moore, Gregory J.

    2016-01-01

    Voxel based morphometry (VBM) is a widely utilized neuroimaging technique for spatially normalizing brain structural MRI (sMRI) onto a common template. The DARTEL technique of VBM takes into account the spatial intensity distribution of sMRIs to construct a study specific group template. The group template is then used to create final individual normalized tissue maps (FINTM) for each subject in the group. In this study, we investigate the effect of group on FINTM, i.e., we evaluate the variability of a constant subject's FINTM when other subjects in the group are iteratively changed. We examine this variability under the following scenarios: (1) when the demographics of the iterative groups are similar, (2) when the average age of the iterative groups is increased, and (3) when the number of subjects with a brain disorder (here we use subjects with autism) is increased. Our results show that when subject demographics of the group remains similar the mean standard deviation (SD) of FINTM gray matter (GM) of the constant subject was around 0.01. As the average age of the group is increased, mean SD of GM increased to around 0.03 and at certain brain locations variability was as high as 0.23. A similar increase in variability was observed when the number of autism subjects in the group was increased where mean SD was around 0.02. Further, we find that autism vs. control GM differences are in the range of −0.05 to +0.05 for more than 97% of the voxels and note that the magnitude of the differences are comparable to GM variability. Finally, we report that opting not to modulate during normalization or increasing the size of the smoothing kernel can decrease FINTM variability but at the loss of subject-specific features. Based on the findings of this study, we outline precautions that should be considered by investigators to reduce the impact of group on FINTM and thereby derive more meaningful group differences when comparing two cohorts of subjects. PMID:27994534

  11. Influence of Group on Individual Subject Maps in SPM Voxel Based Morphometry.

    PubMed

    Michael, Andrew M; Evans, Eli; Moore, Gregory J

    2016-01-01

    Voxel based morphometry (VBM) is a widely utilized neuroimaging technique for spatially normalizing brain structural MRI (sMRI) onto a common template. The DARTEL technique of VBM takes into account the spatial intensity distribution of sMRIs to construct a study specific group template. The group template is then used to create final individual normalized tissue maps (FINTM) for each subject in the group. In this study, we investigate the effect of group on FINTM, i.e., we evaluate the variability of a constant subject's FINTM when other subjects in the group are iteratively changed. We examine this variability under the following scenarios: (1) when the demographics of the iterative groups are similar, (2) when the average age of the iterative groups is increased, and (3) when the number of subjects with a brain disorder (here we use subjects with autism) is increased. Our results show that when subject demographics of the group remains similar the mean standard deviation (SD) of FINTM gray matter (GM) of the constant subject was around 0.01. As the average age of the group is increased, mean SD of GM increased to around 0.03 and at certain brain locations variability was as high as 0.23. A similar increase in variability was observed when the number of autism subjects in the group was increased where mean SD was around 0.02. Further, we find that autism vs. control GM differences are in the range of -0.05 to +0.05 for more than 97% of the voxels and note that the magnitude of the differences are comparable to GM variability. Finally, we report that opting not to modulate during normalization or increasing the size of the smoothing kernel can decrease FINTM variability but at the loss of subject-specific features. Based on the findings of this study, we outline precautions that should be considered by investigators to reduce the impact of group on FINTM and thereby derive more meaningful group differences when comparing two cohorts of subjects.

  12. Widespread structural brain changes in OCD: a systematic review of voxel-based morphometry studies.

    PubMed

    Piras, Federica; Piras, Fabrizio; Chiapponi, Chiara; Girardi, Paolo; Caltagirone, Carlo; Spalletta, Gianfranco

    2015-01-01

    The most widely accepted model of obsessive-compulsive disorder (OCD) assumes brain abnormalities in the "affective circuit", mainly consisting of volume reduction in the medial orbitofrontal, anterior cingulate and temporolimbic cortices, and tissue expansion in the striatum and thalamus. The advent of whole-brain, voxel-based morphometry (VBM) has provided increasing evidence that regions outside the "affective" orbitofronto-striatal circuit are involved in OCD. Nevertheless, potential confounds from the different image analysis methods, as well as other factors, such as patients' medication and comorbidity status, may limit generalization of results. In the present paper, we systematically reviewed the whole-brain VBM literature on OCD by focussing specifically on degree of consistency between studies, extent to which findings have been replicated and interrelation between clinical variables and OCD anatomy, a potentially crucial factor that has been systematically examined only in a limited number of studies. The PubMed database was searched through February 2012. A total of 156 studies were identified; 18 of them fulfilled the inclusion/exclusion criteria and included 511 patients and 504 controls. Results support the notion that the brain alterations responsible for OCD are represented at the network level, and that widespread structural abnormalities may contribute to neurobiological vulnerability to OCD. Apart from defects in regions within the classic "affective" circuit, volume reduction of the cortical source of the dorsolateral (DL) prefronto-striatal "executive" circuit (dorsomedial, DL, ventrolateral and frontopolar prefrontal cortices), and of reciprocally connected regions (temporo-parieto-occipital associative areas) is consistently described in OCD patients. Moreover, increased volume of the internal capsule and reduced frontal and parietal white matter volumes may account for altered anatomical connectivity in fronto-subcortical circuitry

  13. A New Method for Automated Identification and Morphometry of Myelinated Fibers Through Light Microscopy Image Analysis.

    PubMed

    Novas, Romulo Bourget; Fazan, Valeria Paula Sassoli; Felipe, Joaquim Cezar

    2016-02-01

    Nerve morphometry is known to produce relevant information for the evaluation of several phenomena, such as nerve repair, regeneration, implant, transplant, aging, and different human neuropathies. Manual morphometry is laborious, tedious, time consuming, and subject to many sources of error. Therefore, in this paper, we propose a new method for the automated morphometry of myelinated fibers in cross-section light microscopy images. Images from the recurrent laryngeal nerve of adult rats and the vestibulocochlear nerve of adult guinea pigs were used herein. The proposed pipeline for fiber segmentation is based on the techniques of competitive clustering and concavity analysis. The evaluation of the proposed method for segmentation of images was done by comparing the automatic segmentation with the manual segmentation. To further evaluate the proposed method considering morphometric features extracted from the segmented images, the distributions of these features were tested for statistical significant difference. The method achieved a high overall sensitivity and very low false-positive rates per image. We detect no statistical difference between the distribution of the features extracted from the manual and the pipeline segmentations. The method presented a good overall performance, showing widespread potential in experimental and clinical settings allowing large-scale image analysis and, thus, leading to more reliable results.

  14. Morphometry of boar sperm head and flagellum in semen backflow after insemination.

    PubMed

    García-Vázquez, Francisco Alberto; Hernández-Caravaca, Iván; Yánez-Quintana, Wellington; Matás, Carmen; Soriano-Úbeda, Cristina; Izquierdo-Rico, María José

    2015-09-01

    Once deposited in the female reproductive system, sperm begin their competition and undergo a selection to reach the site of fertilization. Little is known about the special characteristics of sperm that reach the oviduct and are able to fertilize, with even less information on the role of sperm dimension and shape in transport and fertilization. Here, we examine whether sperm morphometry could be involved in their journey within the uterus. For this purpose, sperm head dimension (length, width, area, and perimeter) and shape (shape factor, ellipticity, elongation, and regularity), and flagellum length were analyzed in the backflow at different times after insemination (0-15, 16-30, and 31-60 minutes). Sperm morphometry in the backflow was also analyzed taking into account the site of semen deposition (cervical vs. intrauterine). Finally, flagellum length was measured at the uterotubal junction. Sperm analyzed in the backflow were small (head and flagellum) with different head shapes compared with sperm observed in the dose before insemination. The site of deposition influenced head morphometry and tail size both being smaller in the backflow after cervical insemination compared with intrauterine insemination. Mean tail length of sperm collected in the backflow was smaller than that in the insemination dose and at the uterotubal junction. Overall, our results suggest that sperm size may be involved in sperm transport either because of environment or through sperm selection and competence on their way to encounter the female gamete.

  15. Morphometry and mixing regime of a tropical lake: Lake Nova (Southeastern Brazil).

    PubMed

    Gonçalves, Monica A; Garcia, Fábio C; Barroso, Gilberto F

    2016-09-01

    Lake Nova (15.5 km2) is the second largest lake in the Lower Doce River Valley (Southeastern Brazil). A better understanding of ecosystem structure and functioning requires knowledge about lake morphometry, given that lake basin form influences water column stratification. The present study aims to contribute to the understanding of relationship between morphometry and mixing patterns of deep tropical lakes in Brazil. Water column profiles of temperature and dissolved oxygen were taken on four sampling sites along the lake major axis during 2011, 2012 and 2013. The bathymetric survey was carried out in July 2011, along 131.7 km of hydrographic tracks yield 51,692 depth points. Morphometric features of lake size and form factors describe the relative deep subrectangular elongated basin with maximum length of 15.7 km, shoreline development index 5.0, volume of 0.23 km3, volume development of 1.3, and maximum, mean and relative depths of 33.9 m, 14.7 m and 0.7 %, respectively. The deep basin induces a monomictic pattern, with thermal stratification during the wet/warm season associated with anoxic bottom waters (1/3 of lake volume), and mixing during dry and cool season. Based on in situ measurements of tributary river discharges, theoretical retention time (RT) has been estimated in 13.4 years. The morphometry of Lake Nova promote long water RT and the warm monomictic mixing pattern, which is in accordance to the deep tropical lakes in Brazil.

  16. Multivariate Tensor-based Morphometry on Surfaces: Application to Mapping Ventricular Abnormalities in HIV/AIDS

    PubMed Central

    Wang, Yalin; Zhang, Jie; Gutman, Boris; Chan, Tony F.; Becker, James T.; Aizenstein, Howard J.; Lopez, Oscar L.; Tamburo, Robert J.; Toga, Arthur W.; Thompson, Paul M.

    2010-01-01

    Here we developed a new method, called multivariate tensor-based surface morphometry (TBM), and applied it to study lateral ventricular surface differences associated with HIV/AIDS. Using concepts from differential geometry and the theory of differential forms, we created mathematical structures known as holomorphic one-forms, to obtain an efficient and accurate conformal parameterization of the lateral ventricular surfaces in the brain. The new meshing approach also provides a natural way to register anatomical surfaces across subjects, and improves on prior methods as it handles surfaces that branch and join at complex 3D junctions. To analyze anatomical differences, we computed new statistics from the Riemannian surface metrics - these retain multivariate information on local surface geometry. We applied this framework to analyze lateral ventricular surface morphometry in 3D MRI data from 11 subjects with HIV/AIDS and 8 healthy controls. Our method detected a 3D profile of surface abnormalities even in this small sample. Multivariate statistics on the local tensors gave better effect sizes for detecting group differences, relative to other TBM-based methods including analysis of the Jacobian determinant, the largest and smallest eigenvalues of the surface metric, and the pair of eigenvalues of the Jacobian matrix. The resulting analysis pipeline may improve the power of surface-based morphometry studies of the brain. PMID:19900560

  17. Anatomic Variation in Morphometry of Human Coracoid Process among Asian Population.

    PubMed

    Fathi, Manal; Cheah, Pike-See; Ahmad, Umar; Nasir, M Nizlan; San, Aye Aye; Abdul Rahim, Ezamin; Hussin, Paisal; Mahmud, Rozi; Othman, Fauziah

    2017-01-01

    Ethnic origin plays an important role in bone morphometry. Studies examining the influence of coracoid process have focused primarily on adults and have not included people from diverse Asian ethnic backgrounds. Our goal was to explore ethnic differences in morphometry of coracoid among Asian population. We performed morphometric measurements of coracoid process on cadaveric shoulders and shoulder CT scans from 118 specimens. The cadaveric sample included Indian (46%), Chinese (27%), and Myanmarese (27%) subjects, while the CT scans sample included Chinese (67%) and Malay (33%) subjects. The morphometric measurements were performed using digital caliper and software developed at Golden Horses Health Sanctuary (GHHS). In the Indian cadaveric shoulders, the coracoid process is better developed than the other groups with the exception of the tip width of coracoid process. There are significant differences in almost all measurements (P < 0.05) between the ethnic groups. On the other hand, the morphometry of coracoid process from CT scans data is bigger in Chinese than Malay subjects when stratified by sex (P < 0.05). Moreover, in all morphometric measurements, the females had smaller measurements than males (P < 0.05). Understanding such differences is important in anatomy, forensic and biological identity, and orthopaedic and shoulder surgeries.

  18. Unique Ecophysiology among U(VI)-Reducing Bacteria as Revealed by Evaluation of Oxygen Metabolism in Anaeromyxobacter dehalogenans Strain 2CP-C▿ †

    PubMed Central

    Thomas, Sara H.; Sanford, Robert A.; Amos, Benjamin K.; Leigh, Mary Beth; Cardenas, Erick; Löffler, Frank E.

    2010-01-01

    Anaeromyxobacter spp. respire soluble hexavalent uranium, U(VI), leading to the formation of insoluble U(IV), and are present at the uranium-contaminated Oak Ridge Integrated Field Research Challenge (IFC) site. Pilot-scale in situ bioreduction of U(VI) has been accomplished in area 3 of the Oak Ridge IFC site following biostimulation, but the susceptibility of the reduced material to oxidants (i.e., oxygen) compromises long-term U immobilization. Following oxygen intrusion, attached Anaeromyxobacter dehalogenans cells increased approximately 5-fold from 2.2 × 107 ± 8.6 × 106 to 1.0 × 108 ± 2.2 × 107 cells per g of sediment collected from well FW101-2. In the same samples, the numbers of cells of Geobacter lovleyi, a population native to area 3 and also capable of U(VI) reduction, decreased or did not change. A. dehalogenans cells captured via groundwater sampling (i.e., not attached to sediment) were present in much lower numbers (<1.3 × 104 ± 1.1 × 104 cells per liter) than sediment-associated cells, suggesting that A. dehalogenans cells occur predominantly in association with soil particles. Laboratory studies confirmed aerobic growth of A. dehalogenans strain 2CP-C at initial oxygen partial pressures (pO2) at and below 0.18 atm. A negative linear correlation [μ = (−0.09 × pO2) + 0.051; R2 = 0.923] was observed between the instantaneous specific growth rate μ and pO2, indicating that this organism should be classified as a microaerophile. Quantification of cells during aerobic growth revealed that the fraction of electrons released in electron donor oxidation and used for biomass production (fs) decreased from 0.52 at a pO2 of 0.02 atm to 0.19 at a pO2 of 0.18 atm. Hence, the apparent fraction of electrons utilized for energy generation (i.e., oxygen reduction) (fe) increased from 0.48 to 0.81 with increasing pO2, suggesting that oxygen is consumed in a nonrespiratory process at a high pO2. The ability to tolerate high oxygen concentrations

  19. Analysis of the ability of pramlintide to inhibit amyloid formation by human islet amyloid polypeptide reveals a balance between optimal recognition and reduced amyloidogenicity.

    PubMed

    Wang, Hui; Ridgway, Zachary; Cao, Ping; Ruzsicska, Bela; Raleigh, Daniel P

    2015-11-10

    The hormone human islet amyloid polypeptide (hIAPP or amylin) plays a role in glucose metabolism, but forms amyloid in the pancreas in type 2 diabetes (T2D) and is associated with β-cell death and dysfunction in the disease. Inhibitors of islet amyloid have therapeutic potential; however, there are no clinically approved inhibitors, and the mode of action of existing inhibitors is not well understood. Rat IAPP (rIAPP) differs from hIAPP at six positions, does not form amyloid, and is an inhibitor of amyloid formation by hIAPP. Five of the six differences are located within the segment of residues 20-29, and three of them are Pro residues, which are well-known disruptors of β-sheet structure. rIAPP is thus a natural example of a "β-breaker inhibitor", a molecule that combines a recognition element with an entity that inhibits β-sheet formation. Pramlintide (PM) is a peptide drug approved for use as an adjunct to insulin therapy for treatment of diabetes. PM was developed by introducing the three Pro substitutions found in rIAPP into hIAPP. Thus, it more closely resembles the human peptide than does rIAPP. Here we examine and compare the ability of rIAPP, PM, and a set of designed analogues of hIAPP to inhibit amyloid formation by hIAPP, to elucidate the factors that lead to effective peptide-based inhibitors. Our results reveal, for this class of molecules, a balance between the reduced amyloidogenicity of the inhibitory sequence on one hand and its ability to recognize hIAPP on the other.

  20. Analysis of the Ability of Pramlintide to Inhibit Amyloid Formation by Human Islet Amyloid Polypeptide Reveals a Balance between Optimum Recognition and Reduced Amyloidgenicity

    PubMed Central

    Wang, Hui; Ridgway, Zachary; Cao, Ping; Ruzsicska, Bela; Raleigh, Daniel P.

    2015-01-01

    The hormone human islet amyloid polypeptide (hIAPP or amylin) plays a role in glucose metabolism, but forms amyloid in the pancreas in type 2 diabetes (T2D) and is associated with β-cell death and dysfunction in the disease. Inhibitors of islet amyloid have therapeutic potential, however there are no clinically approved inhibitors and the mode of action of existing inhibitors is not well understood. Rat IAPP (rIAPP), differs from hIAPP at six positions, does not form amyloid and is an inhibitor of amyloid formation by hIAPP. Five of the six differences are located within residues 20-29, and three of them are Pro residues, which are well known disruptors of β-sheet structure. rIAPP is thus a natural example of a “β-breaker inhibitor”; a molecule which combines a recognition element with an entity that inhibits β-sheet formation. Pramlintide (PM) is a peptide drug approved for use as an adjunct to insulin therapy for treatment of diabetes. PM was developed by introducing the three Pro substitutions found in rIAPP into hIAPP. Thus, it more closely resembles the human peptide than does rIAPP. Here we examine and compare the ability of rIAPP, PM and a set of designed analogs of hIAPP to inhibit amyloid formation by hIAPP, in order to elucidate the factors which lead to effective peptide based inhibitors. Our results reveal, for this class of molecules, a balance between the reduced amyloidogenicity of the inhibitory sequence on the one hand and its ability to recognize hIAPP on the other. PMID:26407043

  1. Patterns of 15N assimilation and growth of methanotrophic ANME-2 archaea and sulfate-reducing bacteria within structured syntrophic consortia revealed by FISH-SIMS.

    PubMed

    Orphan, Victoria J; Turk, Kendra A; Green, Abigail M; House, Christopher H

    2009-07-01

    Methane release from the oceans is controlled in large part by syntrophic interactions between anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (DSS), frequently found as organized consortia. An understanding of the specifics of this symbiotic relationship and the metabolic heterogeneity existing between and within individual methane-oxidizing aggregates is currently lacking. Here, we use the microanalytical method FISH-SIMS (fluorescence in situ hybridization-secondary ion mass spectrometry) to describe the physiological traits and anabolic activity of individual methanotrophic consortia, specifically tracking (15)N-labelled protein synthesis to examine the effects of organization and size on the metabolic activity of the syntrophic partners. Patterns of (15)N distribution within individual aggregates showed enhanced (15)N assimilation in ANME-2 cells relative to the co-associated DSS revealing a decoupling in anabolic activity between the partners. Protein synthesis in ANME-2 cells was sustained throughout the core of individual ANME-2/DSS consortia ranging in size range from 4 to 20 μm. This indicates that metabolic activity of the methane-oxidizing archaea is not limited to, or noticeably enhanced at the ANME-2/DSS boundary. Overall, the metabolic activity of both syntrophic partners within consortia was greater than activity measured in representatives of the ANME-2 and DSS observed alone, with smaller ANME-2/DSS aggregates displaying a tendency for greater (15)N uptake and doubling times ranging from 3 to 5 months. The combination of (15)N-labelling and FISH-SIMS provides an important perspective on the extent of heterogeneity within methanotrophic aggregates and may aid in constraining predictive models of activity and growth by these syntrophic consortia.

  2. The overlapping brain region accounting for the relationship between procrastination and impulsivity: A voxel-based morphometry study.

    PubMed

    Liu, Peiwei; Feng, Tingyong

    2017-09-30

    Procrastination is a prevalent problematic behavior that brings serious consequences, such as lower levels of health, wealth, and well-being. Previous research has verified that impulsivity is one of the traits most strongly correlated with procrastination. However, little is known about why there is a tight behavioral relationship between them. To address this question, we used voxel-based morphometry (VBM) to explore the common neural substrates between procrastination and impulsivity. In line with previous findings, the behavioral results showed a strong behavioral correlation between procrastination and impulsivity. Neuroimaging results showed impulsivity and procrastination shared the common neurobiological underpinnings in the dorsolateral prefrontal cortex (DLPFC) based on the data from 85 participants (sample 1). Furthermore, the mediation analysis revealed that impulsivity mediated the impact of gray matter (GM) volumes of this overlapping region in the DLPFC on procrastination on another independent 84 participants' data (sample 2). In conclusion, the overlapping brain region in the DLPFC would be responsible for the close relationship between procrastination and impulsivity. As a whole, the present study extends our knowledge on procrastination, and provides a novel perspective to explain the tight impulsivity - procrastination relationship. Copyright © 2017 IBRO. Published by Elsevier Ltd. All rights reserved.

  3. Automated multiscale morphometry of muscle disease from second harmonic generation microscopy using tensor-based image processing.

    PubMed

    Garbe, Christoph S; Buttgereit, Andreas; Schürmann, Sebastian; Friedrich, Oliver

    2012-01-01

    Practically, all chronic diseases are characterized by tissue remodeling that alters organ and cellular function through changes to normal organ architecture. Some morphometric alterations become irreversible and account for disease progression even on cellular levels. Early diagnostics to categorize tissue alterations, as well as monitoring progression or remission of disturbed cytoarchitecture upon treatment in the same individual, are a new emerging field. They strongly challenge spatial resolution and require advanced imaging techniques and strategies for detecting morphological changes. We use a combined second harmonic generation (SHG) microscopy and automated image processing approach to quantify morphology in an animal model of inherited Duchenne muscular dystrophy (mdx mouse) with age. Multiphoton XYZ image stacks from tissue slices reveal vast morphological deviation in muscles from old mdx mice at different scales of cytoskeleton architecture: cell calibers are irregular, myofibrils within cells are twisted, and sarcomere lattice disruptions (detected as "verniers") are larger in number compared to samples from healthy mice. In young mdx mice, such alterations are only minor. The boundary-tensor approach, adapted and optimized for SHG data, is a suitable approach to allow quick quantitative morphometry in whole tissue slices. The overall detection performance of the automated algorithm compares very well with manual "by eye" detection, the latter being time consuming and prone to subjective errors. Our algorithm outperfoms manual detection by time with similar reliability. This approach will be an important prerequisite for the implementation of a clinical image databases to diagnose and monitor specific morphological alterations in chronic (muscle) diseases.

  4. Use of MODIS satellite images for detailed lake morphometry: Application to basins with large water level fluctuations

    NASA Astrophysics Data System (ADS)

    Ovakoglou, George; Alexandridis, Thomas K.; Crisman, Thomas L.; Skoulikaris, Charalampos; Vergos, George S.

    2016-09-01

    Lake morphometry is essential for managing water resources and limnetic ecosystems. For reservoirs that receive high sediment loads, frequent morphometric mapping is necessary to define both the effective life of the reservoir and its water storage capacity for irrigation, power generation, flood control and domestic water supply. The current study presents a methodology for updating the digital depth model (DDM) of lakes and reservoirs with wide intra and interannual fluctuations of water levels using satellite remote sensing. A time series of Terra MODIS satellite images was used to map shorelines formed during the annual water level change cycle, and were validated with concurrent Landsat ETM+ satellite images. The shorelines were connected with in-situ observation of water levels and were treated as elevation contours to produce the DDM using spatial interpolation. The accuracy of the digitized shorelines is within the mapping accuracy of the satellite images, while the resulting DDM is validated using in-situ elevation measurements. Two versions of the DDM were produced to assess the influence of seasonal water fluctuation. Finally, the methodology was applied to Lake Kerkini (Greece) to produce an updated DDM, which was compared with the last available bathymetric survey (1991) and revealed changes in sediment distribution within the lake.

  5. Morphology and Morphometry of the Lung in Corn Snakes (Pantherophis guttatus) Infected with Three Different Strains of Ferlavirus.

    PubMed

    Starck, J M; Neul, A; Schmidt, V; Kolb, T; Franz-Guess, S; Balcecean, D; Pees, M

    2017-03-08

    Ophidian paramyxovirus (ferlavirus) is a global threat to reptilian sauropsids in herpetological collections, with occasional but fatal effects. This study characterizes the effects of three different genetic strains of ferlavirus on the dynamic changes of histology and morphometry of the lung of corn snakes (Pantherophis guttatus). Lungs from 42 corn snakes were either sham-infected or infected experimentally under standardized conditions. From 4 to 49 days after intratracheal inoculation, the lungs were examined qualitatively and quantitatively. Progressive microscopical changes were seen in the lung. Initially, increased numbers of heterophils were observed in the interstitium followed by proliferation and vacuolation of epithelial cells lining faveoli. Electron microscopy revealed loss of type-I pneumocytes, hyperplasia of type-II pneumocytes, and interstitial infiltrates of heterophils and mononuclear cells. With progression of disease the respiratory epithelium was initially overgrown by transformed type-II pneumocytes and later became multilayered. The results of the study suggest that the respiratory capacity of the lungs declines with disease development. The dynamics of disease development and histopathology differed in snakes infected with different ferlavirus genogroups. Animals infected with virus genogroup B developed histopathological changes and morphometric changes more rapidly and of greater intensity than snakes infected with viruses from genogroups A or C.

  6. Impact of image acquisition on voxel-based-morphometry investigations of age-related structural brain changes.

    PubMed

    Streitbürger, Daniel-Paolo; Pampel, André; Krueger, Gunnar; Lepsien, Jöran; Schroeter, Matthias L; Mueller, Karsten; Möller, Harald E

    2014-02-15

    A growing number of magnetic resonance imaging studies employ voxel-based morphometry (VBM) to assess structural brain changes. Recent reports have shown that image acquisition parameters may influence VBM results. For systematic evaluation, gray-matter-density (GMD) changes associated with aging were investigated by VBM employing acquisitions with different radiofrequency head coils (12-channel matrix coil vs. 32-channel array), different pulse sequences (MP-RAGE vs. MP2RAGE), and different voxel dimensions (1mm vs. 0.8mm). Thirty-six healthy subjects, classified as young, middle-aged, or elderly, participated in the study. Two-sample and paired t-tests revealed significant effects of acquisition parameters (coil, pulse sequence, and resolution) on the estimated age-related GMD changes in cortical and subcortical regions. Potential advantages in tissue classification and segmentation were obtained for MP2RAGE. The 32-channel coil generally outperformed the 12-channel coil, with more benefit for MP2RAGE. Further improvement can be expected from higher resolution if the loss in SNR is accounted for. Use of inconsistent acquisition parameters in VBM analyses is likely to introduce systematic bias. Overall, acquisition and protocol changes require careful adaptations of the VBM analysis strategy before generalized conclusion can be drawn.

  7. Different gray matter patterns in chronic schizophrenia and chronic bipolar disorder patients identified using voxel-based morphometry.

    PubMed

    Molina, Vicente; Galindo, Gemma; Cortés, Benjamín; de Herrera, Alba G Seco; Ledo, Ana; Sanz, Javier; Montes, Carlos; Hernández-Tamames, Juan A

    2011-08-01

    Gray matter (GM) volume deficits have been described in patients with schizophrenia (Sz) and bipolar disorder (BD), but to date, few studies have directly compared GM volumes between these syndromes with methods allowing for whole-brain comparisons. We have used structural magnetic resonance imaging (MRI) and voxel-based morphometry (VBM) to compare GM volumes between 38 Sz and 19 BD chronic patients. We also included 24 healthy controls. The results revealed a widespread cortical (dorsolateral and medial prefrontal and precentral) and cerebellar deficit as well as GM deficits in putamen and thalamus in Sz when compared to BD patients. Besides, a subcortical GM deficit was shown by Sz and BD groups when compared to the healthy controls, although a putaminal reduction was only evident in the Sz patients. In this comparison, the BD patients showed a limited cortical and subcortical GM deficit. These results support a partly different pattern of GM deficits associated to chronic Sz and chronic BD, with some degree of overlapping.

  8. Hippocampal Substructural Vulnerability to Sleep Disturbance and Cognitive Impairment in Patients with Chronic Primary Insomnia: Magnetic Resonance Imaging Morphometry

    PubMed Central

    Joo, Eun Yeon; Kim, Hosung; Suh, Sooyeon; Hong, Seung Bong

    2014-01-01

    Study Objectives: Despite compelling evidence from animal studies indicating hippocampal subfield-specific vulnerability to poor sleep quality and related cognitive impairment, there have been no human magnetic resonance imaging (MRI) studies investigating the relationship between hippocampal subfield volume and sleep disturbance. Our aim was to investigate the pattern of volume changes across hippocampal subfields in patients with primary insomnia relative to controls. Design: Pointwise morphometry allowed for volume measurements of hippocampal regions on T1-weighted MRI. Setting: University hospital. Patients: Twenty-seven unmedicated patients (age: 51.2 ± 9.6 y) and 30 good sleepers as controls (50.4 ± 7.1 y). Interventions: N/A. Measurements: We compared hippocampal subfield volumes between patients and controls and correlated volume with clinical and neuropsychological features in patients. Results: Patients exhibited bilateral atrophy across all hippocampal subfields (P < 0.05 corrected). Cornu ammonis (CA) 1 subfield atrophy was associated with worse sleep quality (higher Pittsburgh Sleep Quality Index and higher arousal index of polysomnography) (r < -0.45, P < 0.005). The volume of the combined region, including the dentate gyrus (DG) and CA3-4, negatively correlated with verbal memory, verbal information processing, and verbal fluency in patients (|r| > 0.45, P < 0.05). Hemispheric volume asymmetry of this region (left smaller than right) was associated with impaired verbal domain functions (r = 0.50, P < 0.005). Conclusion: Hippocampal subfield atrophy in chronic insomnia suggests reduced neurogenesis in the dentate gyrus (DG) and neuronal loss in the cornu ammonis (CA) subfields in conditions of sleep fragmentation and related chronic stress condition. Atrophy in the CA3-4-DG region was associated with impaired cognitive functions in patients. These observations may provide insight into pathophysiological mechanisms that make patients with chronic

  9. Replicate and technician variation associated with computer aided bull sperm head morphometry analysis (ASMA).

    PubMed

    Gravance, C G; Garner, D L; Pitt, C; Vishwanath, R; Sax-Gravance, S K; Casey, P J

    1999-04-01

    Associations of abnormal spermatozoa with bull fertility have yielded varying results. Manual methods of analysis are subjective and highly variable within and between technicians, which may account for these differences. Computer-aided sperm head morphometry appears to be a precise method of assessing sperm head dimensions; however, the effects of replication and technician on sperm head morphometry have not been assessed. The objective of this study was to determine the inter- and intra-analysis and technician variation associated with computer-aided bull sperm head morphometry analysis. Semen from 10 bulls was diluted to 200 x 10(6) sperm/mL, and slide smears were prepared and stained using haematoxylin and rose bengal. Each of two technicians analysed 250 images from each slide, 3 times, using computer-aided sperm head morphometry analysis. The morphometric dimensions of area, perimeter, length, width and width/length for individual sperm heads of each analysis were assessed by GLM-ANOVA for effects of bulls, replications and technicians. The coefficient of variation was recorded for each analysis and across replications. The mean coefficients of variation within and between analyses were compared between technicians by GLM-ANOVA. No differences (p > 0.1) between technicians were found between or among bulls for area (29.63 vs. 29.26 micron 2), perimeter (23.73 vs. 23.86 microns), length (8.73 vs. 8.71 microns), width (4.47 vs. 4.46 microns), or width/length (0.51 vs. 0.51). No differences (p > 0.1) between replicates for sperm head dimension were detected within or among bulls for either technician. No intra- or inter-analysis differences (p > 0.1) between technicians on CVs were observed. The mean intra-analysis CVs for all bulls for both technicians were area = 6.9%, perimeter = 4.9%, length = 4.5%, width = 5.6% and width/length = 6.5%. The mean interanalysis CVs for both technicians were area = 3.0%, perimeter = 2.4%, length = 2.0%, width = 2.0%, and width

  10. Blood platelet counts, morphology and morphometry in lions, Panthera leo.

    PubMed

    Du Plessis, L

    2009-09-01

    Due to logistical problems in obtaining sufficient blood samples from apparently healthy animals in the wild in order to establish normal haematological reference values, only limited information regarding the blood platelet count and morphology of free-living lions (Panthera leo) is available. This study provides information on platelet counts and describes their morphology with particular reference to size in two normal, healthy and free-ranging lion populations. Blood samples were collected from a total of 16 lions. Platelet counts, determined manually, ranged between 218 and 358 x 10(9)/l. Light microscopy showed mostly activated platelets of various sizes with prominent granules. At the ultrastructural level the platelets revealed typical mammalian platelet morphology. However, morphometric analysis revealed a significant difference (P < 0.001) in platelet size between the two groups of animals. Basic haematological information obtained in this study may be helpful in future comparative studies between animals of the same species as well as in other felids.

  11. A voxel-based morphometry study of gray matter correlates of facial emotion recognition in bipolar disorder.

    PubMed

    Neves, Maila de Castro L; Albuquerque, Maicon Rodrigues; Malloy-Diniz, Leandro; Nicolato, Rodrigo; Silva Neves, Fernando; de Souza-Duran, Fábio Luis; Busatto, Geraldo; Corrêa, Humberto

    2015-08-30

    Facial emotion recognition (FER) is one of the many cognitive deficits reported in bipolar disorder (BD) patients. The aim of this study was to investigate neuroanatomical correlates of FER impairments in BD type I (BD-I). Participants comprised 21 euthymic BD-I patients without Axis I DSM IV-TR comorbidities and 21 healthy controls who were assessed using magnetic resonance imaging and the Penn Emotion Recognition Test (ER40). Preprocessing of images used DARTEL (diffeomorphic anatomical registration through exponentiated Lie algebra) for optimized voxel-based morphometry in SPM8. Compared with healthy subjects, BD-I patients performed poorly in on the ER40 and had reduced gray matter volume (GMV) in the left orbitofrontal cortex, superior portion of the temporal pole and insula. In the BD-I group, the statistical maps indicated a direct correlation between FER on the ER40 and right middle cingulate gyrus GMV. Our findings are consistent with the previous studies regarding the overlap of multiple brain networks of social cognition and BD neurobiology, particularly components of the anterior-limbic neural network.

  12. The effects of cisplatin on rat spinal ganglia: a study by light and electron microscopy and by morphometry.

    PubMed

    Tomiwa, K; Nolan, C; Cavanagh, J B

    1986-01-01

    Cisplatin given in doses of 0.5-2 mg to Wistar and to Sprague-Dawley rats produced nucleolar segregation of the dense fibrillar from the granular component in spinal root ganglion cells. The nucleolar segregation, found to the same extent in large and small neurons, was confirmed by specific silver staining and by electron microscopy. After repeated doses of 1 mg or 0.5 mg, up to 40% of affected nucleoli were observed by light microscopy. Focal clearing of the nucleoplasm of nuclei also occurred. Disorganisation of ribosomes was found in more severely intoxicated animals, especially in large light cells with shrinkage of the Nissl substance and apparent increase in neurofilaments, the latter occasionally distending the initial segment of the axon, but never extending further. Hypertrophy of the satellite cells with increase in the perineuronal intercellular spaces, often associated with irregular, scalloped nuclear and cell outlines, suggested that neuron shrinkage had occurred. This was confirmed by morphometry and marked alterations were found in nucleolar-to-nuclear and nucleolar-to-cell diameter ratios, nuclear and cell diameters were also somewhat reduced without change in the nucleus-to-cell ratios. Peripheral sensory nerve degeneration was not seen, and the animals died from non-neural causes. The probable role of these events in the production of sensory neuropathy is discussed.

  13. Gray matter changes in right superior temporal gyrus in criminal psychopaths. Evidence from voxel-based morphometry.

    PubMed

    Müller, Jürgen L; Gänssbauer, Susanne; Sommer, Monika; Döhnel, Katrin; Weber, Tatjana; Schmidt-Wilcke, Tobias; Hajak, Göran

    2008-08-30

    "Psychopathy" according to the PCL-R describes a specific subgroup of antisocial personality disorder with a high risk for criminal relapses. Lesion and imaging studies point towards frontal or temporal brain regions connected with disturbed social behavior, antisocial personality disorder (APD) and psychopathy. Morphologically, some studies described a reduced prefrontal brain volume, whereas others reported on temporal lobe atrophy. To further investigate whether participants with psychopathy according to the Psychopathy Checklist-Revised Version (PCL-R) show abnormalities in brain structure, we used voxel-based morphometry (VBM) to investigate region-specific changes in gray matter in 17 forensic male inpatients with high PCL-R scores (PCL-R>28) and 17 male control subjects with low PCL-R scores (PCL<10). We found significant gray matter reductions in frontal and temporal brain regions in psychopaths compared with controls. In particular, we found a highly significant volume loss in the right superior temporal gyrus. This is the first study to show that psychopathy is associated with a decrease in gray matter in both frontal and temporal brain regions, in particular in the right superior temporal gyrus, supporting the hypothesis that a disturbed frontotemporal network is critically involved in the pathogenesis of psychopathy.

  14. Gray matter reduction associated with emotion regulation in female outpatients with major depressive disorder: a voxel-based morphometry study.

    PubMed

    Mak, Amanda K Y; Wong, Michael M C; Han, Shi-Hui; Lee, Tatia M C

    2009-10-01

    Though emotion dysregulation is the key feature in major depressive disorder, and structural changes in brain areas of depressed patients have been found, it is unknown how these regional volume alterations correlate with the ability to regulate emotion in the depressed population. We examined the gray matter concentration (GMC) and volume (GMV) in 17 depressed patients and 17 healthy volunteers using a voxel-based morphometry (VBM) study. Images were acquired using a 1.5 T MRI scanner, and were spatially normalized and segmented. Statistical comparisons were performed using the general linear model. The identified volumetric alterations in the depressed participants were correlated with their performance on an emotion regulation task that involved reduction of positive or negative emotions to emotional pictures that were selected according to their individual ratings. The depressed participants showed specific difficulty in regulating negative emotion, though not positive emotion, which was associated with reduced GMV and concentration in the anterior cingulate cortex (ACC) and the inferior orbitofrontal cortex (OFC). Decreased GMC in the superior temporal cortex was also found in people with major depressive disorder. Abnormal structures in the ACC and OFC and the dysregulation of negative emotion may relate to the pathology of major depressive disorder.

  15. Structure-function correlations in Retinitis Pigmentosa patients with partially preserved vision: a voxel-based morphometry study.

    PubMed

    Rita Machado, Ana; Carvalho Pereira, Andreia; Ferreira, Fábio; Ferreira, Sónia; Quendera, Bruno; Silva, Eduardo; Castelo-Branco, Miguel

    2017-09-12

    Retinitis Pigmentosa is a group of hereditary retinal dystrophy disorders associated with progressive peripheral visual field loss. The impact of this retinal loss in cortical gray matter volume has not been addressed before in Retinitis Pigmentosa patients with low vision. Voxel-based morphometry was applied to study whole brain gray matter volume changes in 27 Retinitis Pigmentosa patients with partially preserved vision and 38 age- and gender-matched normally sighted controls to determine whether peripheral visual loss can lead to changes in gray matter volume. We found significant reductions in gray matter volume that were restricted to the occipital cortex of patients. The anteromedial pattern of reduced gray matter volume in visual primary and association cortices was significantly correlated with the extent of the peripheral visual field deficit in this cohort. Moreover, this pattern was found to be associated with the extent of visual field loss. In summary, we found specific visual cortical gray matter loss in Retinitis Pigmentosa patients associated with their visual function profile. The spatial pattern of gray matter loss is consistent with disuse-driven neuronal atrophy which may have clinical implications for disease management, including prosthetic restoration strategies.

  16. Comparative Transcriptomic Analysis of Rectal Tissue from Beef Steers Revealed Reduced Host Immunity in Escherichia coli O157:H7 Super-Shedders

    PubMed Central

    Wang, Ou; Liang, Guanxiang; McAllister, Tim A.; Plastow, Graham; Stanford, Kim; Selinger, Brent; Guan, Le Luo

    2016-01-01

    Super-shedder cattle are a major disseminator of E. coli O157:H7 into the environment, and the terminal rectum has been proposed as the primary E. coli O157:H7 colonization site. This study aimed to identify host factors that are associated with the super-shedding process by comparing transcriptomic profiles in rectal tissue collected from 5 super-shedder cattle and 4 non-shedder cattle using RNA-Seq. In total, 17,859 ± 354 genes and 399 ± 16 miRNAs were detected, and 11,773 genes were expressed in all animals. Fifty-eight differentially expressed (DE) genes (false discovery rate < 0.05) including 11 up-regulated and 47 down-regulated (log 2 (fold change) ranged from -5.5 to 4.2), and 2 up-regulated DE miRNAs (log 2 (fold change) = 2.1 and 2.5, respectively) were identified in super-shedders compared to non-shedders. Functional analysis of DE genes revealed that 31 down-regulated genes were potentially associated with reduced innate and adaptive immune functions in super-shedders, including 13 lymphocytes membrane receptors, 3 transcription factors and 5 cytokines, suggesting the decreased key host immune functions in the rectal tissue of super-shedders, including decreased quantity and migration of immune cells such as lymphocytes, neutrophils and dendritic cells. The up-regulation of bta-miR-29d-3p and the down regulation of its predicted target gene, regulator of G-protein signaling 13, suggested a potential regulatory role of this miRNA in decreased migration of lymphocytes in super-shedders. Based on these findings, the rectal tissue of super-shedders may inherently exhibit less effective innate and adaptive immune protection. Further study is required to confirm if such effect on host immunity is due to the nature of the host itself or due to actions mediated by E. coli O157:H7. PMID:26959367

  17. Individual differences in regional prefrontal gray matter morphometry and fractional anisotropy are associated with different constructs of executive function.

    PubMed

    Smolker, H R; Depue, B E; Reineberg, A E; Orr, J M; Banich, M T

    2015-01-01

    Although the relationship between structural differences within the prefrontal cortex (PFC) and executive function (EF) has been widely explored in cognitively impaired populations, little is known about this relationship in healthy young adults. Using optimized voxel-based morphometry (VBM), surface-based morphometry (SBM), and fractional anisotropy (FA) we determined the association between regional PFC grey matter (GM) morphometry and white matter tract diffusivity with performance on tasks that tap different aspects of EF as drawn from Miyake et al.'s three-factor model of EF. Reductions in both GM volume (VBM) and cortical folding (SBM) in the ventromedial PFC (vmPFC), ventrolateral PFC (vlPFC), and dorsolateral PFC (dlPFC) predicted better common EF, shifting-specific, and updating-specific performance, respectively. Despite capturing different components of GM morphometry, voxel- and surface-based findings were highly related, exhibiting regionally overlapping relationships with EF. Increased white matter FA in fiber tracts that connect the vmPFC and vlPFC with posterior regions of the brain also predicted better common EF and shifting-specific performance, respectively. These results suggest that the neural mechanisms supporting distinct aspects of EF may differentially rely on distinct regions of the PFC, and at least in healthy young adults, are influenced by regional morphometry of the PFC and the FA of major white matter tracts that connect the PFC with posterior cortical and subcortical regions.

  18. Individual differences in regional prefrontal gray matter morphometry and fractional anisotropy are associated with different constructs of executive function

    PubMed Central

    Smolker, H. R.; Reineberg, A. E.; Orr, J. M.; Banich, M. T.

    2015-01-01

    Although the relationship between structural differences within the prefrontal cortex (PFC) and executive function (EF) has been widely explored in cognitively impaired populations, little is known about this relationship in healthy young adults. Using optimized voxel-based morphometry (VBM), surface-based morphometry (SBM), and fractional anisotropy (FA) we determined the association between regional PFC grey matter (GM) morphometry and white matter tract diffusivity with performance on tasks that tap different aspects of EF as drawn from Miyake et al.’s three-factor model of EF. Reductions in both GM volume (VBM) and cortical folding (SBM) in the ventromedial PFC (vmPFC), ventrolateral PFC (vlPFC), and dorsolateral PFC (dlPFC) predicted better common EF, shifting-specific, and updating-specific performance, respectively. Despite capturing different components of GM morphometry, voxel- and surface-based findings were highly related, exhibiting regionally overlapping relationships with EF. Increased white matter FA in fiber tracts that connect the vmPFC and vlPFC with posterior regions of the brain also predicted better common EF and shifting-specific performance, respectively. These results suggest that the neural mechanisms supporting distinct aspects of EF may differentially rely on distinct regions of the PFC, and at least in healthy young adults, are influenced by regional morphometry of the PFC and the FA of major white matter tracts that connect the PFC with posterior cortical and subcortical regions. PMID:24562372

  19. Global and regional brain volumes normalization in weight-recovered adolescents with anorexia nervosa: preliminary findings of a longitudinal voxel-based morphometry study.

    PubMed

    Bomba, Monica; Riva, Anna; Morzenti, Sabrina; Grimaldi, Marco; Neri, Francesca; Nacinovich, Renata

    2015-01-01

    The recent literature on anorexia nervosa (AN) suggests that functional and structural abnormalities of cortico-limbic areas might play a role in the evolution of the disease. We explored global and regional brain volumes in a cross-sectional and follow-up study on adolescents affected by AN. Eleven adolescents with AN underwent a voxel-based morphometry study at time of diagnosis and immediately after weight recovery. Data were compared to volumes carried out in eight healthy, age and sex matched controls. Subjects with AN showed increased cerebrospinal fluid volumes and decreased white and gray matter volumes, when compared to controls. Moreover, significant regional gray matter decrease in insular cortex and cerebellum was found at time of diagnosis. No regional white matter decrease was found between samples and controls. Correlations between psychological evaluation and insular volumes were explored. After weight recovery gray matter volumes normalized while reduced global white matter volumes persisted.

  20. Exploring the brains of Baduk (Go) experts: gray matter morphometry, resting-state functional connectivity, and graph theoretical analysis

    PubMed Central

    Jung, Wi Hoon; Kim, Sung Nyun; Lee, Tae Young; Jang, Joon Hwan; Choi, Chi-Hoon; Kang, Do-Hyung; Kwon, Jun Soo

    2013-01-01

    One major characteristic of experts is intuitive judgment, which is an automatic process whereby patterns stored in memory through long-term training are recognized. Indeed, long-term training may influence brain structure and function. A recent study revealed that chess experts at rest showed differences in structure and functional connectivity (FC) in the head of caudate, which is associated with rapid best next-move generation. However, less is known about the structure and function of the brains of Baduk experts (BEs) compared with those of experts in other strategy games. Therefore, we performed voxel-based morphometry (VBM) and FC analyses in BEs to investigate structural brain differences and to clarify the influence of these differences on functional interactions. We also conducted graph theoretical analysis (GTA) to explore the topological organization of whole-brain functional networks. Compared to novices, BEs exhibited decreased and increased gray matter volume (GMV) in the amygdala and nucleus accumbens (NA), respectively. We also found increased FC between the amygdala and medial orbitofrontal cortex (mOFC) and decreased FC between the NA and medial prefrontal cortex (mPFC). Further GTA revealed differences in measures of the integration of the network and in the regional nodal characteristics of various brain regions activated during Baduk. This study provides evidence for structural and functional differences as well as altered topological organization of the whole-brain functional networks in BEs. Our findings also offer novel suggestions about the cognitive mechanisms behind Baduk expertise, which involves intuitive decision-making mediated by somatic marker circuitry and visuospatial processing. PMID:24106471

  1. Comparing 3 T and 1.5 T MRI for Tracking Alzheimer's Disease Progression with Tensor-Based Morphometry

    PubMed Central

    Ho, April J.; Hua, Xue; Lee, Suh; Leow, Alex D.; Yanovsky, Igor; Gutman, Boris; Dinov, Ivo D.; Leporé, Natasha; Stein, Jason L.; Toga, Arthur W.; Jack, Clifford R.; Bernstein, Matt A.; Reiman, Eric M.; Harvey, Danielle J.; Kornak, John; Schuff, Norbert; Alexander, Gene E.; Weiner, Michael W.; Thompson, Paul M.

    2009-01-01

    A key question in designing MRI-based clinical trials is how the main magnetic field strength of the scanner affects the power to detect disease effects. In 110 subjects scanned longitudinally at both 3.0 and 1.5 T, including 24 patients with Alzheimer's Disease (AD) [74.8 ± 9.2 years, MMSE: 22.6 ± 2.0 at baseline], 51 individuals with mild cognitive impairment (MCI) [74.1 ± 8.0 years, MMSE: 26.6 ± 2.0], and 35 controls [75.9 ± 4.6 years, MMSE: 29.3 ± 0.8], we assessed whether higher-field MR imaging offers higher or lower power to detect longitudinal changes in the brain, using tensor-based morphometry (TBM) to reveal the location of progressive atrophy. As expected, at both field strengths, progressive atrophy was widespread in AD and more spatially restricted in MCI. Power analysis revealed that, to detect a 25% slowing of atrophy (with 80% power), 37 AD and 108 MCI subjects would be needed at 1.5 T versus 49 AD and 166 MCI subjects at 3 T; however, the increased power at 1.5 T was not statistically significant (α = 0.05) either for TBM, or for SIENA, a related method for computing volume loss rates. Analysis of cumulative distribution functions and false discovery rates showed that, at both field strengths, temporal lobe atrophy rates were correlated with interval decline in Alzheimer's Disease Assessment Scale-cognitive subscale (ADAS-cog), mini-mental status exam (MMSE), and Clinical Dementia Rating sum-of-boxes (CDR-SB) scores. Overall, 1.5 and 3 T scans did not significantly differ in their power to detect neurodegenerative changes over a year. PMID:19780044

  2. Exploring the brains of Baduk (Go) experts: gray matter morphometry, resting-state functional connectivity, and graph theoretical analysis.

    PubMed

    Jung, Wi Hoon; Kim, Sung Nyun; Lee, Tae Young; Jang, Joon Hwan; Choi, Chi-Hoon; Kang, Do-Hyung; Kwon, Jun Soo

    2013-01-01

    One major characteristic of experts is intuitive judgment, which is an automatic process whereby patterns stored in memory through long-term training are recognized. Indeed, long-term training may influence brain structure and function. A recent study revealed that chess experts at rest showed differences in structure and functional connectivity (FC) in the head of caudate, which is associated with rapid best next-move generation. However, less is known about the structure and function of the brains of Baduk experts (BEs) compared with those of experts in other strategy games. Therefore, we performed voxel-based morphometry (VBM) and FC analyses in BEs to investigate structural brain differences and to clarify the influence of these differences on functional interactions. We also conducted graph theoretical analysis (GTA) to explore the topological organization of whole-brain functional networks. Compared to novices, BEs exhibited decreased and increased gray matter volume (GMV) in the amygdala and nucleus accumbens (NA), respectively. We also found increased FC between the amygdala and medial orbitofrontal cortex (mOFC) and decreased FC between the NA and medial prefrontal cortex (mPFC). Further GTA revealed differences in measures of the integration of the network and in the regional nodal characteristics of various brain regions activated during Baduk. This study provides evidence for structural and functional differences as well as altered topological organization of the whole-brain functional networks in BEs. Our findings also offer novel suggestions about the cognitive mechanisms behind Baduk expertise, which involves intuitive decision-making mediated by somatic marker circuitry and visuospatial processing.

  3. Morphometry of the orbital region soft tissues in Down syndrome.

    PubMed

    Sforza, Chiarella; Elamin, Fadil; Dellavia, Claudia; Rosati, Riccardo; Lodetti, Gianluigi; Mapelli, Andrea; Ferrario, Virgilio Ferruccio

    2012-01-01

    The orbital region of subjects with Down syndrome (DS) has been scanty described so far. We wanted to detail the morphologic characteristics of the soft tissue orbital region in Italian and North Sudanese subjects with DS. The three-dimensional coordinates of 10 landmarks on the orbital soft tissues were obtained using computerized anthropometry in 53 Italian and 64 North Sudanese subjects with DS aged 4 to 52 years, and in 461 (Italian) and 682 (North Sudanese) sex- and age-matched controls. From the landmarks, linear distances, ratios, areas, and angles were calculated, z scores computed, and compared by t-tests and analyses of covariance. In North Sudanese DS subjects, intercanthal width and height-to-length ratio were increased; biorbital width, eye height, length, and area were reduced. Eye fissure and orbital inclinations relative to Frankfort plane were reduced, whereas orbital inclinations versus the true horizontal were increased. In Italian DS men, orbital height and height-to-length ratio were increased, eye length was decreased; orbital inclination versus the true horizontal was increased. For almost all measurements, a significant effect of age was found. No effects of sex were found. Ethnic group influenced orbital height, area, and orbital inclination versus Frankfort plane. All paired measurements had similar discrepancies on both sides. The orbital soft tissues of North Sudanese DS subjects differed from those of their reference subjects, but this was only partially true for Italian subjects. The 2 ethnic groups had different alterations in their soft tissue orbital regions that were influenced by age, but not by sex.

  4. Extraction of sandy bedforms features through geodesic morphometry

    NASA Astrophysics Data System (ADS)

    Debese, Nathalie; Jacq, Jean-José; Garlan, Thierry

    2016-09-01

    State-of-art echosounders reveal fine-scale details of mobile sandy bedforms, which are commonly found on continental shelfs. At present, their dynamics are still far from being completely understood. These bedforms are a serious threat to navigation security, anthropic structures and activities, placing emphasis on research breakthroughs. Bedform geometries and their dynamics are closely linked; therefore, one approach is to develop semi-automatic tools aiming at extracting their structural features from bathymetric datasets. Current approaches mimic manual processes or rely on morphological simplification of bedforms. The 1D and 2D approaches cannot address the wide ranges of both types and complexities of bedforms. In contrast, this work attempts to follow a 3D global semi-automatic approach based on a bathymetric TIN. The currently extracted primitives are the salient ridge and valley lines of the sand structures, i.e., waves and mega-ripples. The main difficulty is eliminating the ripples that are found to heavily overprint any observations. To this end, an anisotropic filter that is able to discard these structures while still enhancing the wave ridges is proposed. The second part of the work addresses the semi-automatic interactive extraction and 3D augmented display of the main lines structures. The proposed protocol also allows geoscientists to interactively insert topological constraints.

  5. Comparative Gastric Morphometry of Muong Indigenous and Vietnamese Wild Pigs

    PubMed Central

    Trang, Pham Hong; Ooi, Peck Toung; Zuki, Abu Bakar Zakaria; Noordin, Mustapha Mohamed

    2012-01-01

    It is hypothesized that despite sharing a similar habitat, the Muong indigenous and Vietnamese wild pigs may reveal different gastric morphology. Due to the protective nature of procuring these pigs, a total of 12 Muong indigenous pigs and nine Vietnamese wild pigs stomach collected post mortem were analysed for selected biometric parameters and histology. The result indicated that the stomach of the Vietnamese wild pig is broader with a bigger capacity and greater proportion of proper gastric glands. Interestingly, the stomach mass correlated well with live body weight in both breeds apart from possessing similar histomorphometry of the gastric gland regions. On the other hand, the thicker (P < 0.05) submucosa in the Vietnamese wild pig is attributed to the presence of numerous loose connective tissues, abundant blood vessels, adipose tissues and nerve plexus. The appearance of lymphoid follicles underneath the tubular gastric glands in the Vietnamese wild pig exceeded that of Muong indigenous pigs. This finding suggested that the difference in feeding behavior as well as immunity. In conclusion, adaptations found in the Vietnamese wild pig indicated that this breed is equipped with a bigger and effectively functional stomach to suit its digestive physiology and immunity in the wild. PMID:23093914

  6. Computer-assisted sperm head morphometry analysis (ASMA) of cryopreserved ram spermatozoa.

    PubMed

    Gravance, C G; Champion, Z J; Casey, P J

    1998-04-15

    Normal sperm morphology has been shown to be indicative of male fertility; however, subjective methods of assessing morphology are highly variable. Computer-assisted sperm morphometry analysis (ASMA) has been developed for the objective analysis of sperm head dimensions. Developing applicable protocols for sperm head morphometry analysis increases the efficiency of these systems. The objective of the current study was to develop accurate methods for employing ASMA of ram sperm heads. Staining methods, optimal sperm sample numbers microscopic magnification and sampling variation within and between technicians were assessed. Frozen semen from 10 fertile rams was thawed and prepared on slides for morphometric analysis. Staining spermatozoa with hematoxylin and rose bengal stains yielded the best results. Ram sperm head morphometry was accurately evaluated on at least 100 spermatozoa at x 40 objective magnification. Using these techniques, a sample could be analyzed in approximately 3 min. No significant differences in sperm head measurements were detected between 2 technicians. The system properly recognized and digitized ram spermatozoa 95% of the time. The morphometric measurements of sperm heads for all rams were as follows: length = 8.08 microns, width = 4.80 microns, width:length ratio = 0.59, area = 29.13 micron 2 and perimeter = 23.93 microns. The mean within analysis coefficients of variation for all individual analyses and parameters ranged from 4.8% for length to 6.0% for area. The variation between replicate analysis was 2.4% or less for both technicians. When applying proper sample preparation and analysis procedures no differences in measurements or variation were observed between the 2 system operators.

  7. The morphometry of Lake Palmas, a deep natural lake in Brazil.

    PubMed

    Barroso, Gilberto F; Gonçalves, Monica A; Garcia, Fábio da C

    2014-01-01

    Lake Palmas (A = 10.3km2) is located in the Lower Doce River Valley (LDRV), on the southeastern coast of Brazil. The Lake District of the LDRV includes 90 lakes, whose basic geomorphology is associated with the alluvial valleys of the Barreiras Formation (Cenozoic, Neogene) and with the Holocene coastal plain. This study aimed to investigate the relationship of morphometry and thermal pattern of a LDRV deep lake, Lake Palmas. A bathymetric survey carried out in 2011 and the analysis of hydrographic and wind data with a geographic information system allowed the calculation of several metrics of lake morphometry. The vertical profiling of physical and chemical variables in the water column during the wet/warm and dry/mild cold seasons of 2011 to 2013 has furnished a better understanding of the influence of the lake morphometry on its structure and function. The overdeepened basin has a subrectangular elongated shape and is aligned in a NW-SE direction in an alluvial valley with a maximum depth (Zmax) of 50.7 m, a volume of 2.2×10(8) m3 (0.22 km3) and a mean depth (Zmv) of 21.4m. These metrics suggest Lake Palmas as the deepest natural lake in Brazil. Water column profiling has indicated strong physical and chemical stratification during the wet/warm season, with a hypoxic/anoxic layer occupying one-half of the lake volume. The warm monomictic pattern of Lake Palmas, which is in an accordance to deep tropical lakes, is determined by water column mixing during the dry and mild cold season, especially under the influence of a high effective fetch associated with the incidence of cold fronts. Lake Palmas has a very long theoretical retention time, with a mean of 19.4 years. The changes observed in the hydrological flows of the tributary rivers may disturb the ecological resilience of Lake Palmas.

  8. Brain Morphometry on Congenital Hand Deformities based on Teichmüller Space Theory.

    PubMed

    Peng, Hao; Wang, Xu; Duan, Ye; Frey, Scott H; Gu, Xianfeng

    2015-01-01

    Congenital Hand Deformities (CHD) are usually occurred between fourth and eighth week after the embryo is formed. Failure of the transformation from arm bud cells to upper limb can lead to an abnormal appearing/functioning upper extremity which is presented at birth. Some causes are linked to genetics while others are affected by the environment, and the rest have remained unknown. CHD patients develop prehension through the use of their hands, which affect the brain as time passes. In recent years, CHD have gain increasing attention and researches have been conducted on CHD, both surgically and psychologically. However, the impacts of CHD on brain structure are not well-understood so far. Here, we propose a novel approach to apply Teichmüller space theory and conformal welding method to study brain morphometry in CHD patients. Conformal welding signature reflects the geometric relations among different functional areas on the cortex surface, which is intrinsic to the Riemannian metric, invariant under conformal deformation, and encodes complete information of the functional area boundaries. The computational algorithm is based on discrete surface Ricci flow, which has theoretic guarantees for the existence and uniqueness of the solutions. In practice, discrete Ricci flow is equivalent to a convex optimization problem, therefore has high numerically stability. In this paper, we compute the signatures of contours on general 3D surfaces with surface Ricci flow method, which encodes both global and local surface contour information. Then we evaluated the signatures of pre-central and post-central gyrus on healthy control and CHD subjects for analyzing brain cortical morphometry. Preliminary experimental results from 3D MRI data of CHD/control data demonstrate the effectiveness of our method. The statistical comparison between left and right brain gives us a better understanding on brain morphometry of subjects with Congenital Hand Deformities, in particular, missing

  9. The Morphometry of Lake Palmas, a Deep Natural Lake in Brazil

    PubMed Central

    Barroso, Gilberto F.; Gonçalves, Monica A.; Garcia, Fábio da C.

    2014-01-01

    Lake Palmas (A = 10.3km2) is located in the Lower Doce River Valley (LDRV), on the southeastern coast of Brazil. The Lake District of the LDRV includes 90 lakes, whose basic geomorphology is associated with the alluvial valleys of the Barreiras Formation (Cenozoic, Neogene) and with the Holocene coastal plain. This study aimed to investigate the relationship of morphometry and thermal pattern of a LDRV deep lake, Lake Palmas. A bathymetric survey carried out in 2011 and the analysis of hydrographic and wind data with a geographic information system allowed the calculation of several metrics of lake morphometry. The vertical profiling of physical and chemical variables in the water column during the wet/warm and dry/mild cold seasons of 2011 to 2013 has furnished a better understanding of the influence of the lake morphometry on its structure and function. The overdeepened basin has a subrectangular elongated shape and is aligned in a NW-SE direction in an alluvial valley with a maximum depth (Zmax) of 50.7m, a volume of 2.2×108 m3 (0.22km3) and a mean depth (Zmv) of 21.4m. These metrics suggest Lake Palmas as the deepest natural lake in Brazil. Water column profiling has indicated strong physical and chemical stratification during the wet/warm season, with a hypoxic/anoxic layer occupying one-half of the lake volume. The warm monomictic pattern of Lake Palmas, which is in an accordance to deep tropical lakes, is determined by water column mixing during the dry and mild cold season, especially under the influence of a high effective fetch associated with the incidence of cold fronts. Lake Palmas has a very long theoretical retention time, with a mean of 19.4 years. The changes observed in the hydrological flows of the tributary rivers may disturb the ecological resilience of Lake Palmas. PMID:25406062

  10. Brain Morphometry on Congenital Hand Deformities based on Teichmüller Space Theory

    PubMed Central

    Peng, Hao; Wang, Xu; Duan, Ye; Frey, Scott H.; Gu, Xianfeng

    2016-01-01

    Congenital Hand Deformities (CHD) are usually occurred between fourth and eighth week after the embryo is formed. Failure of the transformation from arm bud cells to upper limb can lead to an abnormal appearing/functioning upper extremity which is presented at birth. Some causes are linked to genetics while others are affected by the environment, and the rest have remained unknown. CHD patients develop prehension through the use of their hands, which affect the brain as time passes. In recent years, CHD have gain increasing attention and researches have been conducted on CHD, both surgically and psychologically. However, the impacts of CHD on brain structure are not well-understood so far. Here, we propose a novel approach to apply Teichmüller space theory and conformal welding method to study brain morphometry in CHD patients. Conformal welding signature reflects the geometric relations among different functional areas on the cortex surface, which is intrinsic to the Riemannian metric, invariant under conformal deformation, and encodes complete information of the functional area boundaries. The computational algorithm is based on discrete surface Ricci flow, which has theoretic guarantees for the existence and uniqueness of the solutions. In practice, discrete Ricci flow is equivalent to a convex optimization problem, therefore has high numerically stability. In this paper, we compute the signatures of contours on general 3D surfaces with surface Ricci flow method, which encodes both global and local surface contour information. Then we evaluated the signatures of pre-central and post-central gyrus on healthy control and CHD subjects for analyzing brain cortical morphometry. Preliminary experimental results from 3D MRI data of CHD/control data demonstrate the effectiveness of our method. The statistical comparison between left and right brain gives us a better understanding on brain morphometry of subjects with Congenital Hand Deformities, in particular, missing

  11. Multispectral brain morphometry in Tourette syndrome persisting into adulthood

    PubMed Central

    Martino, Davide; Cavanna, Andrea E.; Hutton, Chloe; Orth, Michael; Robertson, Mary M.; Critchley, Hugo D.; Frackowiak, Richard S.

    2010-01-01

    Tourette syndrome is a childhood-onset neuropsychiatric disorder with a high prevalence of attention deficit hyperactivity and obsessive-compulsive disorder co-morbidities. Structural changes have been found in frontal cortex and striatum in children and adolescents. A limited number of morphometric studies in Tourette syndrome persisting into adulthood suggest ongoing structural alterations affecting frontostriatal circuits. Using cortical thickness estimation and voxel-based analysis of T1- and diffusion-weighted structural magnetic resonance images, we examined 40 adults with Tourette syndrome in comparison with 40 age- and gender-matched healthy controls. Patients with Tourette syndrome showed relative grey matter volume reduction in orbitofrontal, anterior cingulate and ventrolateral prefrontal cortices bilaterally. Cortical thinning extended into the limbic mesial temporal lobe. The grey matter changes were modulated additionally by the presence of co-morbidities and symptom severity. Prefrontal cortical thickness reduction correlated negatively with tic severity, while volume increase in primary somatosensory cortex depended on the intensity of premonitory sensations. Orbitofrontal cortex volume changes were further associated with abnormal water diffusivity within grey matter. White matter analysis revealed changes in fibre coherence in patients with Tourette syndrome within anterior parts of the corpus callosum. The severity of motor tics and premonitory urges had an impact on the integrity of tracts corresponding to cortico-cortical and cortico-subcortical connections. Our results provide empirical support for a patho-aetiological model of Tourette syndrome based on developmental abnormalities, with perturbation of compensatory systems marking persistence of symptoms into adulthood. We interpret the symptom severity related grey matter volume increase in distinct functional brain areas as evidence of ongoing structural plasticity. The convergence of

  12. Characterization of Human Torso Vascular Morphometry in Normotensive and Hypotensive Trauma Patients

    DTIC Science & Technology

    2016-07-01

    2 AWARD NUMBER: W81XWH-14-2-0126 TITLE: Characterization of Human Torso Vascular Morphometry in Normotensive and Hypotensive Trauma Patients...DATES COVERED 06/30/2015-06/29/2016 4. TITLE AND SUBTITLE 5a. CONTRACT NUMBER W81XWH-14-2-0126 Characterization of Human Torso Vascular...DOD vascular 59355 CT ABDOMEN PELVIS W IV CONTRAST 46 White M 1/24/13 20:41 136 130 DOD vascular 59369 CT OUTSIDE FILM CONSULT BRAIN 33

  13. Neural correlates of anxiety in healthy volunteers: a voxel-based morphometry study.

    PubMed

    Spampinato, Maria Vittoria; Wood, Jacqueline N; De Simone, Veronica; Grafman, Jordan

    2009-01-01

    Studies have shown that the amygdala, temporal, and prefrontal cortices play a key role in the expression of anxiety. The correlation between gray matter volume of these structures and behavioral anxiety measures was not previously investigated in healthy volunteers. The authors used voxel-based morphometry to assess the relationship between brain regional volume and anxiety. The authors found an inverse correlation between anxiety measures and cortical volume in regions of the limbic system and prefrontal cortex implicated in the pathogenesis of anxiety disorders. The authors suggest that volumetric variability of these regions may have a correlation with the development of an anxious personality trait.

  14. Morphometry and distribution of isolated caves as a guide for phreatic and confined paleohydrological conditions

    NASA Astrophysics Data System (ADS)

    Frumkin, Amos; Fischhendler, Itay

    2005-04-01

    Isolated caves are a special cave type common in most karst terrains, formed by prolonged slow water flow where aggressivity is locally boosted. The morphometry and distribution of isolated caves are used here to reconstruct the paleohydrology of a karstic mountain range. Within a homogenous karstic rock sequence, two main types of isolated caves are distinguished, and each is associated with a special hydrogeologic setting: maze caves form by rising water in the confined zone of the aquifer, under the Mt. Scopus Group (Israel) confinement, while chamber caves are formed in phreatic conditions, apparently by lateral flow mixing with a vadose input from above.

  15. Combining the boundary shift integral and tensor-based morphometry for brain atrophy estimation

    NASA Astrophysics Data System (ADS)

    Michalkiewicz, Mateusz; Pai, Akshay; Leung, Kelvin K.; Sommer, Stefan; Darkner, Sune; Sørensen, Lauge; Sporring, Jon; Nielsen, Mads

    2016-03-01

    Brain atrophy from structural magnetic resonance images (MRIs) is widely used as an imaging surrogate marker for Alzheimers disease. Their utility has been limited due to the large degree of variance and subsequently high sample size estimates. The only consistent and reasonably powerful atrophy estimation methods has been the boundary shift integral (BSI). In this paper, we first propose a tensor-based morphometry (TBM) method to measure voxel-wise atrophy that we combine with BSI. The combined model decreases the sample size estimates significantly when compared to BSI and TBM alone.

  16. Kinetic of magnetic nanoparticles uptake evaluated by morphometry of mice peritoneal cells

    NASA Astrophysics Data System (ADS)

    Silva, L. P.; Kuckelhaus, S.; Guedes, M. H. A.; Lacava, Z. G. M.; Tedesco, A. C.; Morais, P. C.; Azevedo, R. B.

    2005-03-01

    The development of magnetic fluids (MFs) has led to a wide range of new biomedical applications. Nevertheless, few studies have examined the kinetics of the magnetic nanoparticles (MNPs) internalization by phagocytes. In this study, we present morphometry as a method to quantify the cell surface covered by MNPs. The maximum cell surface covered by MNPs aggregates was 32.5% (8.5 min), 18.3% (24.1 min), and 18.0% (20.2 min) in DMSA, citric acid and dextran-coated MNPs, respectively. We concluded that the phagocytosis process of MNPs is strongly dependent upon the coating species.

  17. Abnormal cerebellar morphometry in abstinent adolescent marijuana users

    PubMed Central

    Medina, Krista Lisdahl; Nagel, Bonnie J.; Tapert, Susan F.

    2010-01-01

    Background Functional neuroimaging data from adults have, in general, found frontocerebellar dysfunction associated with acute and chronic marijuana (MJ) use (Loeber & Yurgelun-Todd, 1999). One structural neuroimaging study found reduced cerebellar vermis volume in young adult MJ users with a history of heavy polysubstance use (Aasly et al., 1993). The goal of this study was to characterize cerebellar volume in adolescent chronic MJ users following one month of monitored abstinence. Method Participants were MJ users (n=16) and controls (n=16) aged 16-18 years. Extensive exclusionary criteria included history of psychiatric or neurologic disorders. Drug use history, neuropsychological data, and structural brain scans were collected after 28 days of monitored abstinence. Trained research staff defined cerebellar volumes (including three cerebellar vermis lobes and both cerebellar hemispheres) on high-resolution T1-weighted magnetic resonance images. Results Adolescent MJ users demonstrated significantly larger inferior posterior (lobules VIII-X) vermis volume (p<.009) than controls, above and beyond effects of lifetime alcohol and other drug use, gender, and intracranial volume. Larger vermis volumes were associated with poorer executive functioning (p’s<.05). Conclusions Following one month of abstinence, adolescent MJ users had significantly larger posterior cerebellar vermis volumes than non-using controls. These greater volumes are suggested to be pathological based on linkage to poorer executive functioning. Longitudinal studies are needed to examine typical cerebellar development during adolescence and the influence of marijuana use. PMID:20413277

  18. Spatial distribution and morphometry of permafrost-related landforms in the Central Pyrenees

    NASA Astrophysics Data System (ADS)

    Fernandes, Marcelo; Oliva, Marc; Lopes, Luís; Ruiz-Fernández, Jesus; Palma, Pedro; Pereira, Paulo

    2017-04-01

    corresponds to the highest parts of the cirques, oscillating between 2700 m a.s.l. for protalus lobes and 2900 m a.s.l. for rock glaciers. Nevertheless, 77% of the rock glaciers and 78% of the protalus lobes are located in the elevation belt ranging from 2200 to 2600 m a.s.l., which is assumed to be the optimal elevation range for their development in the study area. Aspect does not show any prevailing orientation in the case of rock glaciers, though protalus lobe formed preferably on SW aspects (27%), being almost absent in the S, SE and E aspects (only 5%). Regarding morphometry, the average area occupied by the rock glaciers decreases with altitude (6.4 ha to 1.2 ha). This trend is not observed in the case of protalus lobes, which show the largest surfaces between 2200 and 2600 m a.s.l. The W/L ratio reveals that the rock glaciers distributed at lower altitudes are more elongated (W/L ratio > 2), while those at higher elevations are shorter. No clear patterns are observed when comparing the morphology of protalus lobes and the altitude. The average slope of both landforms lies between 21-22°, with a maximum of 29° for rock glaciers and 31° for protalus lobes. The minimum slope necessary for the development of these two landforms is 11°. The geomorphological mapping of the glacial landforms that is being now conducted will allow identifying the chronology of the development of these landforms based on its chronostratigraphic position within the valley and with respect to the four moraine complexes (glacial stages) identified in the area.

  19. Visceral sensitivity correlates with decreased regional gray matter volume in healthy volunteers: a voxel-based morphometry study.

    PubMed

    Elsenbruch, Sigrid; Schmid, Julia; Kullmann, Jennifer S; Kattoor, Joswin; Theysohn, Nina; Forsting, Michael; Kotsis, Vassilios

    2014-02-01

    Regional changes in brain structure have been reported in patients with altered visceral sensitivity and chronic abdominal pain, such as in irritable bowel syndrome. It remains unknown whether structural brain changes are associated with visceral sensitivity. Therefore, we present the first study in healthy individuals to address whether interindividual variations in gray matter volume (GMV) in pain-relevant regions correlate with visceral sensitivity. In 92 healthy young adults (52 female), we assessed rectal sensory and pain thresholds and performed voxel-based morphometry (VBM) to compute linear regression models with visceral sensory and pain thresholds, respectively, as independent variable and GMV in a priori-defined regions of interest (ROIs) as dependent variable. All results were familywise error (FWE) corrected at a level of PFWE<.05 and covaried for age. The mean (±SEM) rectal thresholds were 14.78±0.46mm Hg for first sensation and 33.97±1.13mm Hg for pain, without evidence of sex differences. Lower rectal sensory threshold (ie, increased sensitivity) correlated significantly with reduced GMV in the thalamus, insula, posterior cingulate cortex, ventrolateral and orbitofrontal prefrontal cortices, amygdala, and basal ganglia (all PFWE<.05). Lower rectal pain threshold was associated with reduced GMV in the right thalamus (PFWE=.051). These are the first data supporting that increased visceral sensitivity correlates with decreased gray matter volume in pain-relevant brain regions. These findings support that alterations in brain morphology not only occur in clinical pain conditions but also occur according to normal interindividual variations in visceral sensitivity. Copyright © 2013 International Association for the Study of Pain. Published by Elsevier B.V. All rights reserved.

  20. Analysis of the morphometry and variations in the extensor digitorum brevis muscle: an anatomic guide for muscle flap and tendon transfer surgical dissection

    PubMed Central

    Sirasanagandla, Srinivasa Rao; Nayak, Satheesha B.; Somayaji, Nagabhooshana S.; Rao, Mohandas K. G.; Bhat, Kumar M. R.

    2013-01-01

    The extensor digitorum brevis muscle (EDB) is a practical option for use as an island flap or free flap when reconstructing soft tissue defects in the ankle as well as in the entire lower limb. It is frequently used to correct crossover toe deformity and other painful toe disorders. We evaluated the morphometry of the EDB in 44 formalin-fixed limbs. Length and width of the muscles were measured. Surface area was calculated as the product of length and width of the muscle. The length of each tendon was also measured from its origin to the point of distal attachment. Presence of any additional tendons was noted. Mean length, width, and surface area of the muscle were 7.39±0.71 cm, 4.1±0.37 cm, and 30.5±4.78 cm2 on the right side and 7.2±0.84 cm, 3.9±0.37 cm, and 28.4±5.35 cm2 on the left side, respectively. Morphometry of the tendons revealed that the tendon of the great toe had the highest mean length (9.5 cm) and the tendon of the fourth toe had the lowest mean length (6.3 cm). Four of the limbs studied (9.09%) had only three tendons. Three of the limbs studied (6.81%) had five tendons, and in one exceptional case (2.27%), six tendons were detected. These observations have significant value and are applicable to plastic and orthopedic surgery. PMID:24179695

  1. Andean Basins Morphometry: Assesing South American Large Rivers' Source Areas

    NASA Astrophysics Data System (ADS)

    Bean, R. A.; Latrubesse, E. M.

    2014-12-01

    Presently there are no regional-scale morphometric analyses of Andean fluvial basins. Therefore, we created a continental-scale database of these basins. Our data covers over an area 1,000,000 km2 of the Andes, from Venezuela to Argentina. These basins are the source of some of the largest rivers in the world including the Amazon, Orinoco, Parana, and Magdalena. Morphometric parameters including shape factor, relief ratio, longitudinal profiles and different indices of basin elevation were calculated based on the CGIAR SRTM 4.1 DEM (~90 m resolution). FAO Hydrosheds were used to segment the DEM by major catchment and then manually cut at the Andean zone. In the North and Central Andes, this produced over 500,000 subcatchments, which we reduced to 619 by setting minimum catchment area to 100 km2. We then integrate lithologic data from DNPM geologic data. Our results indicate that sedimentary lithologies dominate Central Andean catchments (n=268,k=4), which cover an area 767,00 km2, while the Northern Andean catchments (covering 350,000 km2) are more varied, dominated by volcanics in the Pacific (n=78), a sedimentary (48%) dominant mix in the Caribbean (n=138) and 60% sedimentary in the Amazon-Orinoco subregion catchments (n=138). Elevation averages are smallest in the north Andes and average maximum elevations (6,026 m) in the Argentinian catchments (n=65) of the Central Andes are the highest. Shape factors range from 0.49 to 0.58 in the North and 0.52 to 0.58 in the Central Andes. There are clear differences in all categories between region and subregion, but that difference does not hinge on a single morphometric or geologic parameter. Morphometric parameters at a watershed scale (listed in Table) are analyzed and hydrologic data from gauging stations throughout the Andes (n=100) are used to compare morphometric parameters with lithology and characteristics from the basin hydrograph (peak discharge timing, minimum and maximum discharge, and runoff).

  2. Stem Transcriptome Reveals Mechanisms to Reduce the Energetic Cost of Shade-Avoidance Responses in Tomato1[C][W][OA

    PubMed Central

    Cagnola, Juan Ignacio; Ploschuk, Edmundo; Benech-Arnold, Tomás; Finlayson, Scott A.; Casal, Jorge José

    2012-01-01

    While the most conspicuous response to low red/far-red ratios (R:FR) of shade light perceived by phytochrome is the promotion of stem growth, additional, less obvious effects may be discovered by studying changes in the stem transcriptome. Here, we report rapid and reversible stem transcriptome responses to R:FR in tomato (Solanum lycopersicum). As expected, low R:FR promoted the expression of growth-related genes, including those involved in the metabolism of cell wall carbohydrates and in auxin responses. In addition, genes involved in flavonoid synthesis, isoprenoid metabolism, and photosynthesis (dark reactions) were overrepresented in clusters showing reduced expression in the stem of low R:FR-treated plants. Consistent with these responses, low R:FR decreased the levels of flavonoids (anthocyanin, quercetin, kaempferol) and selected isoprenoid derivatives (chlorophyll, carotenoids) in the stem and severely reduced the photosynthetic capacity of this organ. However, lignin contents were unaffected. Low R:FR reduced the stem levels of jasmonate, which is a known inducer of flavonoid synthesis. The rate of stem respiration was also reduced in low R:FR-treated plants, indicating that by downsizing the stem photosynthetic apparatus and the levels of photoprotective pigments under low R:FR, tomato plants reduce the energetic cost of shade-avoidance responses. PMID:22872775

  3. Lake Morphometry for NHD Lakes in the Western Portion of the South Atlantic-Gulf Region 3 HUC

    EPA Pesticide Factsheets

    Lake morphometry metrics are known to influence productivity in lakes and are important for building various types of ecological and environmental models of lentic systems. The lake morphometry dataset included here contains estimates of Surface Area, Shoreline Length, Shoreline Development, Maximum Depth, Mean Depth, Lake Volume, Maximum Lake Length, Mean Lake Width, Maximum Lake Width, and Fetch for each of the ??lakepond?? waterbodies in the NHDPlus V2. The current release of the datasets is version 0.1 and future refinements to the data are expected.

  4. Lake Morphometry for NHD Lakes in the Southern Portion of the South Atlantic-Gulf Region 3 HUC

    EPA Pesticide Factsheets

    Lake morphometry metrics are known to influence productivity in lakes and are important for building various types of ecological and environmental models of lentic systems. The lake morphometry dataset included here contains estimates of Surface Area, Shoreline Length, Shoreline Development, Maximum Depth, Mean Depth, Lake Volume, Maximum Lake Length, Mean Lake Width, Maximum Lake Width, and Fetch for each of the ??lakepond?? waterbodies in the NHDPlus V2. The current release of the datasets is version 0.1 and future refinements to the data are expected.

  5. Lake Morphometry for NHD Lakes in the Northern Portion of the South Atlantic-Gulf Region 3 HUC

    EPA Pesticide Factsheets

    Lake morphometry metrics are known to influence productivity in lakes and are important for building various types of ecological and environmental models of lentic systems. The lake morphometry dataset included here contains estimates of Surface Area, Shoreline Length, Shoreline Development, Maximum Depth, Mean Depth, Lake Volume, Maximum Lake Length, Mean Lake Width, Maximum Lake Width, and Fetch for each of the ??lakepond?? waterbodies in the NHDPlus V2. The current release of the datasets is version 0.1 and future refinements to the data are expected.

  6. The structure of an orthorhombic crystal form of a 'forced reduced' thiol peroxidase reveals lattice formation aided by the presence of the affinity tag.

    PubMed

    Beckham, Katherine S H; Byron, Olwyn; Roe, Andrew J; Gabrielsen, Mads

    2012-05-01

    Thiol peroxidase (Tpx) is an atypical 2-Cys peroxiredoxin, which has been suggested to be important for cell survival and virulence in Gram-negative pathogens. The structure of a catalytically inactive version of this protein in an orthorhombic crystal form has been determined by molecular replacement. Structural alignments revealed that Tpx is conserved. Analysis of the crystal packing shows that the linker region of the affinity tag is important for formation of the crystal lattice.

  7. Lake morphometry and wind exposure may shape the plankton community structure in acidic mining lakes.

    PubMed

    Weithoff, Guntram; Moser, Michael; Kamjunke, Norbert; Gaedke, Ursula; Weisse, Thomas

    2010-05-01

    Acidic mining lakes (pH <3) are specific habitats exhibiting particular chemical and biological characteristics. The species richness is low and mixotrophy and omnivory are common features of the plankton food web in such lakes. The plankton community structure of mining lakes of different morphometry and mixing type but similar chemical characteristics (Lake 130, Germany and Lake Langau, Austria) was investigated. The focus was laid on the species composition, the trophic relationship between the phago-mixotrophic flagellate Ochromonas sp. and bacteria and the formation of a deep chlorophyll maximum along a vertical pH-gradient. The shallow wind-exposed Lake 130 exhibited a higher species richness than Lake Langau. This increase in species richness was made up mainly by mero-planktic species, suggesting a strong benthic/littoral - pelagic coupling. Based on the field data from both lakes, a nonlinear, negative relation between bacteria and Ochromonas biomass was found, suggesting that at an Ochromonas biomass below 50 μg C L(-1), the grazing pressure on bacteria is low and with increasing Ochromonas biomass bacteria decline. Furthermore, in Lake Langau, a prominent deep chlorophyll maximum was found with chlorophyll concentrations ca. 50 times higher than in the epilimnion which was build up by the euglenophyte Lepocinclis sp. We conclude that lake morphometry, and specific abiotic characteristics such as mixing behaviour influence the community structure in these mining lakes.

  8. Generalized tensor-based morphometry of HIV/AIDS using multivariate statistics on deformation tensors.

    PubMed

    Lepore, N; Brun, C; Chou, Y Y; Chiang, M C; Dutton, R A; Hayashi, K M; Luders, E; Lopez, O L; Aizenstein, H J; Toga, A W; Becker, J T; Thompson, P M

    2008-01-01

    This paper investigates the performance of a new multivariate method for tensor-based morphometry (TBM). Statistics on Riemannian manifolds are developed that exploit the full information in deformation tensor fields. In TBM, multiple brain images are warped to a common neuroanatomical template via 3-D nonlinear registration; the resulting deformation fields are analyzed statistically to identify group differences in anatomy. Rather than study the Jacobian determinant (volume expansion factor) of these deformations, as is common, we retain the full deformation tensors and apply a manifold version of Hotelling's $T(2) test to them, in a Log-Euclidean domain. In 2-D and 3-D magnetic resonance imaging (MRI) data from 26 HIV/AIDS patients and 14 matched healthy subjects, we compared multivariate tensor analysis versus univariate tests of simpler tensor-derived indices: the Jacobian determinant, the trace, geodesic anisotropy, and eigenvalues of the deformation tensor, and the angle of rotation of its eigenvectors. We detected consistent, but more extensive patterns of structural abnormalities, with multivariate tests on the full tensor manifold. Their improved power was established by analyzing cumulative p-value plots using false discovery rate (FDR) methods, appropriately controlling for false positives. This increased detection sensitivity may empower drug trials and large-scale studies of disease that use tensor-based morphometry.

  9. Small volcanoes in Tempe Terra, Mars: Their detailed morphometry and inferred geologic significance

    NASA Technical Reports Server (NTRS)

    Davis, P. A.; Tanaka, K. L.

    1993-01-01

    The Tempe Terra province contains a variety of volcanic landforms that range in size from small vents (less than 10 km in diameter) to moderately sized volcanoes (150 km in diameter). The volcanoes are aligned along the dominant northerly and northeasterly trends of the faults in this region, and many of the volcanoes occur on grabens. Some workers have speculated on the nature of some of the volcanoes on the basis of their general morphology, shadow measurement height, lateral dimension, and geologic setting. As part of a larger study, we have obtained detailed photoclinometric profiles across five of the more conspicuous small volcanoes in the Tempe Terra region. For these data, we extracted for each volcano its flank width and edifice height and the width and depth of its summit crater. We statistically compared these dimensions for each volcano with a set of average dimensions for each type of terrestrial volcanic feature listed in Pike and Clow (1981). These comparisons indicate that the morphometries of the Martian volcanoes 1, 2, and 3 most closely match Earth's cratered basaltic lava shields, and the morphometries of volcanoes 4 and 5 are similar to those of terrestrial basaltic tuff rings.

  10. Recreational marijuana use impacts white matter integrity and subcortical (but not cortical) morphometry.

    PubMed

    Orr, Joseph M; Paschall, Courtnie J; Banich, Marie T

    2016-01-01

    A recent shift in legal and social attitudes toward marijuana use has also spawned a surge of interest in understanding the effects of marijuana use on the brain. There is considerable evidence that an adolescent onset of marijuana use negatively impacts white matter coherence. On the other hand, a recent well-controlled study demonstrated no effects of marijuana use on the morphometry of subcortical or cortical structures when users and non-users were matched for alcohol use. Regardless, most studies have involved small, carefully selected samples, so the ability to generalize to larger populations is limited. In an attempt to address this issue, we examined the effects of marijuana use on white matter integrity and cortical and subcortical morphometry using data from the Human Connectome Project (HCP) consortium. The HCP data consists of ultra-high resolution neuroimaging data from a large community sample, including 466 adults reporting recreational marijuana use. Rather than just contrasting two groups of individuals who vary significantly in marijuana usage as typifies prior studies, we leveraged the large sample size provided by the HCP data to examine parametric effects of recreational marijuana use. Our results indicate that the earlier the age of onset of marijuana use, the lower was white matter coherence. Age of onset also also affected the shape of the accumbens, while the number of lifetime uses impacted the shape of the amygdala and hippocampus. Marijuana use had no effect on cortical volumes. These findings suggest subtle but significant effects of recreational marijuana use on brain structure.

  11. A case study of morphometry as a more sensitive paleoceanographic tool in Globigerinoides ruber

    NASA Astrophysics Data System (ADS)

    Iwai, F. S.; de Lima Toledo, F. A.; Badaraco Costa, K.

    2013-12-01

    There are a number of paleoceanographic tools that take advantage from the wide geographic and temporal occurrence of planktic foraminifers in marine sediments. These tools comprises since simple visual identification and counting to geochemical analysis. Globigerinoides ruber is specially employed due to its high abundance in addition to the advantages mentioned above. That has been attributed to its broad tolerance to most of ecological factors and due to this fact, for this reason, its abundance fluctuation does not provide a significant paleocenographic data like other species do. Globigerinoides ruber has been largely employed in geochemical analysis which demands a higher number of individuals. However, Globigerinoides ruber from brazilian continental margin core tops sediments presents no significant fluctuation either in its abundance and on two of the main paleoceanographic proxies, oxygen and carbon isotope signals, indicating there is no significant environmental difference along brazilian continental margin. Nevertheless, Globigerinoides ruber specimens morphometry does show a significant change between brazilian continental margin core tops. This indicates that morphometry may be a more sensitive tool, enabling a more detailed exploration of paleoceanographical data than other tools do in this species.

  12. Analysis of shallow landslides by morphometry parameters derived from terrestrial laser scanning point clouds

    NASA Astrophysics Data System (ADS)

    Mayr, A.; Rutzinger, M.; Bremer, M.; Wiegand, C.; Kringer, K.; Geitner, C.

    2012-04-01

    Erosion by shallow landslides is a widespread and growing phenomenon in mountainous areas. The major consequences are loss of soil and regolith as well as damages on infrastructure and provision of unconsolidated material for secondary processes such as mudflows. In this study we present a concept for extracting morphometry parameters from terrestrial laser scanning (TLS) point clouds in order to investigate the relation between slope surface structure and regolith depth. TLS is used to collect high-resolution point cloud data of an affected slope in the Schmirn Valley (Tyrol, Austria). Regolith depth is considered to be one of the important factors for the development of shallow landslides. However, direct field measurements are labour- and time-consuming. In this study we developed an approach, to investigate the relation between regolith depth and surface morphometry parameters. The reference regolith depth information is derived from lightweight dynamic cone penetrometer tests (DCPT) within the test site. The suggested approach integrates spatial analysis of Geographic Information Systems and point cloud processing algorithms. It will help to enhance the prediction of shallow landslide occurrence by (i) deriving high resolution 3D morphometric parameters and (ii) determining regolith depth with a reasonable effort due to automation. In future we want to be able to contribute with this concept to the detailed modelling of shallow landslide susceptibility on alpine slopes.

  13. Analysis of histological and immunohistochemical patterns of benign and malignant adrenocortical tumors by computerized morphometry.

    PubMed

    Dalino Ciaramella, Paolo; Vertemati, Maurizio; Petrella, Duccio; Bonacina, Edgardo; Grossrubatscher, Erika; Duregon, Eleonora; Volante, Marco; Papotti, Mauro; Loli, Paola

    2017-07-01

    Diagnosis of benign and purely localized malignant adrenocortical lesions is still a complex issue. Moreover, histology-based diagnosis may suffer of a moment of subjectivity due to inter- and intra-individual variations. The aim of the present study was to assess, by computerized morphometry, the morphological features in benign and malignant adrenocortical neoplasms. Eleven adrenocortical adenomas (ACA) were compared with 18 adrenocortical cancers (ACC). All specimens were stained with H&E, cellular proliferation marker Ki-67 and reticulin. We generated a morphometric model based on the analysis of volume fractions occupied by Ki-67 positive and negative cells (nuclei and cytoplasm), vascular and inflammatory compartment; we also analyzed the surface fraction occupied by reticulin. We compared the quantitative data of Ki-67 obtained by morphometry with the quantification resulting from pathologist's visual reading. The volume fraction of Ki-67 positive cells in ACCs was higher than in ACAs. The volume fraction of nuclei in unit volume and the nuclear/cytoplasmic ratio in both Ki-67 negative cells and Ki-67 positive cells were prominent in ACCs. The surface fraction of reticulin was considerably lower in ACCs. Our computerized morphometric model is simple, reproducible and can be used by the pathologist in the histological workup of adrenocortical tumors to achieve precise and reader-independent quantification of several morphological characteristics of adrenocortical tumors. Copyright © 2017 Elsevier GmbH. All rights reserved.

  14. Lake morphometry and wind exposure may shape the plankton community structure in acidic mining lakes

    PubMed Central

    Weithoff, Guntram; Moser, Michael; Kamjunke, Norbert; Gaedke, Ursula; Weisse, Thomas

    2011-01-01

    Acidic mining lakes (pH <3) are specific habitats exhibiting particular chemical and biological characteristics. The species richness is low and mixotrophy and omnivory are common features of the plankton food web in such lakes. The plankton community structure of mining lakes of different morphometry and mixing type but similar chemical characteristics (Lake 130, Germany and Lake Langau, Austria) was investigated. The focus was laid on the species composition, the trophic relationship between the phago-mixotrophic flagellate Ochromonas sp. and bacteria and the formation of a deep chlorophyll maximum along a vertical pH-gradient. The shallow wind-exposed Lake 130 exhibited a higher species richness than Lake Langau. This increase in species richness was made up mainly by mero-planktic species, suggesting a strong benthic/littoral – pelagic coupling. Based on the field data from both lakes, a nonlinear, negative relation between bacteria and Ochromonas biomass was found, suggesting that at an Ochromonas biomass below 50 μg C L−1, the grazing pressure on bacteria is low and with increasing Ochromonas biomass bacteria decline. Furthermore, in Lake Langau, a prominent deep chlorophyll maximum was found with chlorophyll concentrations ca. 50 times higher than in the epilimnion which was build up by the euglenophyte Lepocinclis sp. We conclude that lake morphometry, and specific abiotic characteristics such as mixing behaviour influence the community structure in these mining lakes. PMID:23225914

  15. Active immunization against GnRH in pre-pubertal domestic mammals: testicular morphometry, histopathology and endocrine responses in rabbits, guinea pigs and ram lambs.

    PubMed

    Aponte, P M; Gutierrez-Reinoso, M A; Sanchez-Cepeda, E G; Garcia-Herreros, M

    2017-08-24

    Effective tools for male contraception are important in the control of reproduction in animal populations. The aim of the present study was to evaluate the effects of active immunization against gonadotropin-releasing hormone (GnRH) on male reproductive function assessing testicular morphological changes and serum-gonadotropin levels in pre-pubertal rabbits, guinea pigs and ram lambs. An anti-GnRH vaccine was developed by linking a GnRH-homologous molecule to a tetanus clostridial toxoid (Al(OH)3 coadjuvant). After vaccination protocols testicular morphometry, histopathological alterations and endocrine responses (FSH, LH, testosterone and cortisol serum levels) were evaluated. Testicular volume was significantly reduced in vaccinated animals with respect to the control group in rabbits, guinea pigs and ram lambs (P<0.05 to P<0.001). The anti-GnRH vaccine generated a reduction in testicular volume of 15-, 27- and 11-fold, respectively. Tubule diameters decreased in the vaccinated group with respect to the control ~2.0-, 1.2- and 3.5-fold, respectively (P<0.001). Tubule, intertubular and lumen volumes significantly decreased in vaccinated rabbits (P<0.05), guinea pigs and ram lambs (P<0.01). Vaccinated animals of the three species showed significant reductions in spermatogonial numbers (10- to 40-fold; P<0.01). Sperm was absent in all seminiferous tubules of all rabbits, and most individuals of guinea pigs (80%) and ram lambs (60%). No significant differences were observed between vaccinated and control groups regarding FSH and LH during the experiments in the three experimental species/models used. Testosterone, however, was only significantly lower (~22-fold, P<0.01) in vaccinated rabbits. In conclusion, the present study demonstrated that pre-pubertal active immunization against GnRH leads to endocrine disruption and marked differences on testicular morphometry, development and activity among lagomorphs, hystricomorphs and ovine species with species

  16. From Cortical and Subcortical Grey Matter Abnormalities to Neurobehavioral Phenotype of Angelman Syndrome: A Voxel-Based Morphometry Study.

    PubMed

    Aghakhanyan, Gayane; Bonanni, Paolo; Randazzo, Giovanna; Nappi, Sara; Tessarotto, Federica; De Martin, Lara; Frijia, Francesca; De Marchi, Daniele; De Masi, Francesco; Kuppers, Beate; Lombardo, Francesco; Caramella, Davide; Montanaro, Domenico

    2016-01-01

    Angelman syndrome (AS) is a rare neurogenetic disorder due to loss of expression of maternal ubiquitin-protein ligase E3A (UBE3A) gene. It is characterized by severe developmental delay, speech impairment, movement or balance disorder and typical behavioral uniqueness. Affected individuals show normal magnetic resonance imaging (MRI) findings, although mild dysmyelination may be observed. In this study, we adopted a quantitative MRI analysis with voxel-based morphometry (FSL-VBM) method to investigate disease-related changes in the cortical/subcortical grey matter (GM) structures. Since 2006 to 2013 twenty-six AS patients were assessed by our multidisciplinary team. From those, sixteen AS children with confirmed maternal 15q11-q13 deletions (mean age 7.7 ± 3.6 years) and twenty-one age-matched controls were recruited. The developmental delay and motor dysfunction were assessed using Bayley III and Gross Motor Function Measure (GMFM). Principal component analysis (PCA) was applied to the clinical and neuropsychological datasets. High-resolution T1-weighted images were acquired and FSL-VBM approach was applied to investigate differences in the local GM volume and to correlate clinical and neuropsychological changes in the regional distribution of GM. We found bilateral GM volume loss in AS compared to control children in the striatum, limbic structures, insular and orbitofrontal cortices. Voxel-wise correlation analysis with the principal components of the PCA output revealed a strong relationship with GM volume in the superior parietal lobule and precuneus on the left hemisphere. The anatomical distribution of cortical/subcortical GM changes plausibly related to several clinical features of the disease and may provide an important morphological underpinning for clinical and neurobehavioral symptoms in children with AS.

  17. Morphometry and pattern of a large sample of Canadian eskers: new insights into ice sheet meltwater drainage

    NASA Astrophysics Data System (ADS)

    Storrar, Robert; Stokes, Chris; Evans, David

    2013-04-01

    Meltwater drainage systems beneath ice sheets are a poorly understood, yet fundamentally important environment for understanding glacier dynamics, which are strongly influenced by the nature and quantity of meltwater entering the subglacial system. Contemporary sub-ice sheet meltwater drainage systems are notoriously difficult to access and monitor, but it is possible to utilise the exposed beds of past ice sheets to further our understanding of subglacial drainage. In particular, eskers record deposition in glacial drainage channels and are widespread on the exposed beds of former ice sheets, although they have rarely been studied in detail at the ice sheet scale. This paper presents the results of a remote sensing investigation of a large sample (>20,000) of eskers mapped from Landsat imagery of Canada and formed under the North American Ice Sheet Complex. Within a GIS framework, we investigate their spatial arrangement and morphometry, including length, fragmentation, sinuosity, spacing, frequency and tributaries. Results indicate that the channels in which eskers formed were often very long (hundreds of km) and often very straight (mean sinuosity approximates 1). In some locations, the lateral distance between neighbouring eskers is remarkably consistent and results indicate a preferred spacing of around 12 km. In other locations, typically over soft sediments, esker patterns are more chaotic, as predicted by theory. Significantly, comparison to an existing ice margin chronology reveals that the meltwater drainage system of the ice sheet became more organised and efficient during deglaciation: the number of eskers at the ice margin increased as deglaciation progressed and eskers became more closely spaced. The data presented in this paper provide an alternative perspective on the problems surrounding ice sheet meltwater drainage and are particularly suitable for: (i), assessment of the factors that control esker location and formation; (ii), rigorous testing of

  18. From Cortical and Subcortical Grey Matter Abnormalities to Neurobehavioral Phenotype of Angelman Syndrome: A Voxel-Based Morphometry Study

    PubMed Central

    Aghakhanyan, Gayane; Bonanni, Paolo; Randazzo, Giovanna; Nappi, Sara; Tessarotto, Federica; De Martin, Lara; Frijia, Francesca; De Marchi, Daniele; De Masi, Francesco; Kuppers, Beate; Lombardo, Francesco; Caramella, Davide; Montanaro, Domenico

    2016-01-01

    Angelman syndrome (AS) is a rare neurogenetic disorder due to loss of expression of maternal ubiquitin-protein ligase E3A (UBE3A) gene. It is characterized by severe developmental delay, speech impairment, movement or balance disorder and typical behavioral uniqueness. Affected individuals show normal magnetic resonance imaging (MRI) findings, although mild dysmyelination may be observed. In this study, we adopted a quantitative MRI analysis with voxel-based morphometry (FSL-VBM) method to investigate disease-related changes in the cortical/subcortical grey matter (GM) structures. Since 2006 to 2013 twenty-six AS patients were assessed by our multidisciplinary team. From those, sixteen AS children with confirmed maternal 15q11-q13 deletions (mean age 7.7 ± 3.6 years) and twenty-one age-matched controls were recruited. The developmental delay and motor dysfunction were assessed using Bayley III and Gross Motor Function Measure (GMFM). Principal component analysis (PCA) was applied to the clinical and neuropsychological datasets. High-resolution T1-weighted images were acquired and FSL-VBM approach was applied to investigate differences in the local GM volume and to correlate clinical and neuropsychological changes in the regional distribution of GM. We found bilateral GM volume loss in AS compared to control children in the striatum, limbic structures, insular and orbitofrontal cortices. Voxel-wise correlation analysis with the principal components of the PCA output revealed a strong relationship with GM volume in the superior parietal lobule and precuneus on the left hemisphere. The anatomical distribution of cortical/subcortical GM changes plausibly related to several clinical features of the disease and may provide an important morphological underpinning for clinical and neurobehavioral symptoms in children with AS. PMID:27626634

  19. Effects of minocycline add-on treatment on brain morphometry and cerebral perfusion in recent-onset schizophrenia.

    PubMed

    Chaves, Cristiano; Marque, Cristiane R; Maia-de-Oliveira, João P; Wichert-Ana, Lauro; Ferrari, Thiago B; Santos, Antonio C; Araújo, David; Machado-de-Sousa, João P; Bressan, Rodrigo A; Elkis, Helio; Crippa, José A; Guimarães, Francisco S; Zuardi, Antônio W; Baker, Glen B; Dursun, Serdar M; Hallak, Jaime E C

    2015-02-01

    Increasing evidence suggests that the tetracycline antibiotic minocycline has neuroprotective effects and is a potential treatment for schizophrenia. However, the mechanisms of action of minocycline in the CNS remain elusive. The aim of this study was to investigate the effects of minocycline on brain morphology and cerebral perfusion in patients with recent-onset schizophrenia after 12months of a randomized double-blind, placebo-controlled clinical trial of minocycline add-on treatment. This study included 24 outpatients with recent-onset schizophrenia randomized for 12months of adjuvant treatment with minocycline (200mg/d) or placebo. MRI (1.5T) and [(99m)Tc]-ECD SPECT brain scans were performed at the end of the 12-month of trial. Between-condition comparisons of SPECT and MRI brain images were performed using statistical parametric mapping and analyzed by voxel-based morphometry (VBM). Minocycline adjuvant treatment significantly reduced positive and negative symptoms when compared with placebo. The VBM analysis of MRI scans showed that the patients in the placebo group had significant lower gray matter volumes in the midposterior cingulate cortex and in the precentral gyrus in comparison with the patients in the minocycline group. In addition, a decreased ECD uptake in the minocycline condition was observed in fronto-temporal areas. These results suggest that minocycline may protect against gray matter loss and modulate fronto-temporal areas involved in the pathophysiology of schizophrenia. Furthermore, minocycline add-on treatment may be a potential treatment in the early stages of schizophrenia and may ameliorate clinical deterioration and brain alterations observed in this period.

  20. Global brain atrophy and corticospinal tract alterations in ALS, as investigated by voxel-based morphometry of 3-D MRI.

    PubMed

    Kassubek, Jan; Unrath, Alexander; Huppertz, Hans-Jürgen; Lulé, Dorothée; Ethofer, Thomas; Sperfeld, Anne-Dorte; Ludolph, Albert C

    2005-12-01

    In ALS, advanced magnetic resonance imaging (MRI) techniques are increasingly used to investigate the underlying pathology. In this study, the technique of voxel-based morphometry (VBM) was applied to 3-D MRI data in ALS patients to localize regional grey and white matter changes. Twenty-two ALS patients (mean age 58+/-9 years) with clinically definite ALS by revised El Escorial criteria were studied. None of the patients had any signs of associated frontotemporal dementia. High-resolution 3-D MRI data sets of the whole brain, collected on a 1.5 T scanner, were analysed by statistical parametric mapping (SPM) and VBM in comparison to an age-matched normal data base consisting of 22 healthy volunteers (mean age 59+/-11 years), for grey matter and white matter segments separately. Global brain atrophy was assessed by calculation of brain parenchymal fractions (BPF). In ALS patients, BPF were significantly reduced compared to controls (p = 0.0003), indicating global brain atrophy. Regional decreases of grey matter density were found in the ALS patients at corrected p<0.01 in the right-hemispheric primary motor cortex (area of the highest Z-score) and in the left medial frontal gyrus. Furthermore, regional white matter alterations were observed along the corticospinal tracts bilaterally and in multiple smaller areas including corpus callosum, cerebellum, frontal and occipital subcortical regions. Besides considerable global atrophy in ALS, the topography of ALS-associated cerebral morphological changes could be mapped using VBM, in particular white matter signal changes along the bilateral corticospinal tracts, but also in extra-motor areas. VBM might be a potential tool to visualize disease progression in future longitudinal studies.

  1. Dyslexia and voxel-based morphometry: correlations between five behavioural measures of dyslexia and gray and white matter volumes.

    PubMed

    Tamboer, Peter; Scholte, H Steven; Vorst, Harrie C M

    2015-10-01

    In voxel-based morphometry studies of dyslexia, the relation between causal theories of dyslexia and gray matter (GM) and white matter (WM) volume alterations is still under debate. Some alterations are consistently reported, but others failed to reach significance. We investigated GM alterations in a large sample of Dutch students (37 dyslexics and 57 non-dyslexics) with two analyses: group differences in local GM and total GM and WM volume and correlations between GM and WM volumes and five behavioural measures. We found no significant group differences after corrections for multiple comparisons although total WM volume was lower in the group of dyslexics when age was partialled out. We presented an overview of uncorrected clusters of voxels (p < 0.05, cluster size k > 200) with reduced or increased GM volume. We found four significant correlations between factors of dyslexia representing various behavioural measures and the clusters found in the first analysis. In the whole sample, a factor related to performances in spelling correlated negatively with GM volume in the left posterior cerebellum. Within the group of dyslexics, a factor related to performances in Dutch-English rhyme words correlated positively with GM volume in the left and right caudate nucleus and negatively with increased total WM volume. Most of our findings were in accordance with previous reports. A relatively new finding was the involvement of the caudate nucleus. We confirmed the multiple cognitive nature of dyslexia and suggested that experience greatly influences anatomical alterations depending on various subtypes of dyslexia, especially in a student sample.

  2. Neural Correlates of Aggression in Medication-Naive Children with ADHD: Multivariate Analysis of Morphometry and Tractography.

    PubMed

    Cha, Jiook; Fekete, Tomer; Siciliano, Francesco; Biezonski, Dominik; Greenhill, Laurence; Pliszka, Steven R; Blader, Joseph C; Roy, Amy Krain; Leibenluft, Ellen; Posner, Jonathan

    2015-06-01

    Aggression is widely observed in children with attention deficit/hyperactivity disorder (ADHD) and has been frequently linked to frustration or the unsatisfied anticipation of reward. Although animal studies and human functional neuroimaging implicate altered reward processing in aggressive behaviors, no previous studies have documented the relationship between fronto-accumbal circuitry-a critical cortical pathway to subcortical limbic regions-and aggression in medication-naive children with ADHD. To address this, we collected behavioral measures and parental reports of aggression and impulsivity, as well as structural and diffusion MRI, from 30 children with ADHD and 31 healthy controls (HC) (mean age, 10±2.1 SD). Using grey matter morphometry and probabilistic tractography combined with multivariate statistical modeling (partial least squares regression and support vector regression), we identified anomalies within the fronto-accumbal circuit in childhood ADHD, which were associated with increased aggression. More specifically, children with ADHD showed reduced right accumbal volumes and frontal-accumbal white matter connectivity compared with HC. The magnitude of the accumbal volume reductions within the ADHD group was significantly correlated with increased aggression, an effect mediated by the relationship between the accumbal volume and impulsivity. Furthermore, aggression, but not impulsivity, was significantly explained by multivariate measures of fronto-accumbal white matter connectivity and cortical thickness within the orbitofrontal cortex. Our multi-modal imaging, combined with multivariate statistical modeling, indicates that the fronto-accumbal circuit is an important substrate of aggression in children with ADHD. These findings suggest that strategies aimed at probing the fronto-accumbal circuit may be beneficial for the treatment of aggressive behaviors in childhood ADHD.

  3. Elevated Left and Reduced Right Orbitomedial Prefrontal Fractional Anisotropy in Adults With Bipolar Disorder Revealed by Tract-Based Spatial Statistics

    PubMed Central

    Versace, Amelia; Almeida, Jorge R. C.; Hassel, Stefanie; Walsh, Nicholas D.; Novelli, Massimiliano; Klein, Crystal R.; Kupfer, David J.; Phillips, Mary L.

    2009-01-01

    Context Diffusion tensor imaging (DTI) studies in adults with bipolar disorder (BD) indicate altered white matter (WM) in the orbitomedial prefrontal cortex (OMPFC), potentially underlying abnormal prefrontal corticolimbic connectivity and mood dysregulation in BD. Objective To use tract-based spatial statistics (TBSS) to examine WM skeleton (ie, the most compact whole-brain WM) in subjects with BD vs healthy control subjects. Design Cross-sectional, case-control, whole-brain DTI using TBSS. Setting University research institute. Participants Fifty-six individuals, 31 having a DSM-IV diagnosis of BD type I (mean age, 35.9 years [age range, 24-52 years]) and 25 controls (mean age, 29.5 years [age range, 19-52 years]). Main Outcome Measures Fractional anisotropy (FA) longitudinal and radial diffusivities in subjects with BD vs controls (covarying for age) and their relationships with clinical and demographic variables. Results Subjects with BD vs controls had significantly greater FA (t>3.0, P≤.05 corrected) in the left uncinate fasciculus (reduced radial diffusivity distally and increased longitudinal diffusivity centrally), left optic radiation (increased longitudinal diffusivity), and right anterothalamic radiation (no significant diffusivity change). Subjects with BD vs controls had significantly reduced FA (t>3.0, P≤.05 corrected) in the right uncinate fasciculus (greater radial diffusivity). Among subjects with BD, significant negative correlations (P<.01) were found between age and FA in bilateral uncinate fasciculi and in the right anterothalamic radiation, as well as between medication load and FA in the left optic radiation. Decreased FA (P<.01) was observed in the left optic radiation and in the right anterothalamic radiation among subjects with BD taking vs those not taking mood stabilizers, as well as in the left optic radiation among depressed vs remitted subjects with BD. Subjects having BD with vs without lifetime alcohol or other drug abuse had

  4. Uranium Bio-accumulation and Cycling as revealed by Uranium Isotopes in Naturally Reduced Sediments from the Upper Colorado River Basin

    NASA Astrophysics Data System (ADS)

    Lefebvre, Pierre; Noël, Vincent; Jemison, Noah; Weaver, Karrie; Bargar, John; Maher, Kate

    2016-04-01

    Uranium (U) groundwater contamination following oxidized U(VI) releases from weathering of mine tailings is a major concern at numerous sites across the Upper Colorado River Basin (CRB), USA. Uranium(IV)-bearing solids accumulated within naturally reduced zones (NRZs) characterized by elevated organic carbon and iron sulfide compounds. Subsequent re-oxidation of U(IV)solid to U(VI)aqueous then controls the release to groundwater and surface water, resulting in plume persistence and raising public health concerns. Thus, understanding the extent of uranium oxidation and reduction within NRZs is critical for assessing the persistence of the groundwater contamination. In this study, we measured solid-phase uranium isotope fractionation (δ238/235U) of sedimentary core samples from four study sites (Shiprock, NM, Grand Junction, Rifle and Naturita, CO) using a multi-collector inductively coupled plasma mass spectrometer (MC-ICP-MS). We observe a strong correlation between U accumulation and the extent of isotopic fractionation, with Δ238U up to +1.8 ‰ between uranium-enriched and low concentration zones. The enrichment in the heavy isotopes within the NRZs appears to be especially important in the vadose zone, which is subject to variations in water table depth. According to previous studies, this isotopic signature is consistent with biotic reduction processes associated with metal-reducing bacteria. Positive correlations between the amount of iron sulfides and the accumulation of reduced uranium underline the importance of sulfate-reducing conditions for U(IV) retention. Furthermore, the positive fractionation associated with U reduction observed across all sites despite some variations in magnitude due to site characteristics, shows a regional trend across the Colorado River Basin. The maximum extent of 238U enrichment observed in the NRZ proximal to the water table further suggests that the redox cycling of uranium, with net release of U(VI) to the groundwater by

  5. DEVELOPMENT OF THE SMALL AIRWAYS AND ALVEOLI FROM CHILDHOOD TO ADULT LUNG MEASURED BY AEROSOL-DERIVED AIRWAY MORPHOMETRY

    EPA Science Inventory

    Understanding the human development of pulmonary airspaces is important for calculating the dose from exposure to inhaled materials as a function of age. We have measured, in vivo, the airspace caliber of the small airways and alveoli by aerosol-derived airway morphometry (ADAM) ...

  6. Dyslexia and Voxel-Based Morphometry: Correlations between Five Behavioural Measures of Dyslexia and Gray and White Matter Volumes

    ERIC Educational Resources Information Center

    Tamboer, Peter; Scholte, H. Steven; Vorst, Harrie C. M.

    2015-01-01

    In voxel-based morphometry studies of dyslexia, the relation between causal theories of dyslexia and gray matter (GM) and white matter (WM) volume alterations is still under debate. Some alterations are consistently reported, but others failed to reach significance. We investigated GM alterations in a large sample of Dutch students (37 dyslexics…

  7. DEVELOPMENT OF THE SMALL AIRWAYS AND ALVEOLI FROM CHILDHOOD TO ADULT LUNG MEASURED BY AEROSOL-DERIVED AIRWAY MORPHOMETRY

    EPA Science Inventory

    Understanding the human development of pulmonary airspaces is important for calculating the dose from exposure to inhaled materials as a function of age. We have measured, in vivo, the airspace caliber of the small airways and alveoli by aerosol-derived airway morphometry (ADAM) ...

  8. Dyslexia and Voxel-Based Morphometry: Correlations between Five Behavioural Measures of Dyslexia and Gray and White Matter Volumes

    ERIC Educational Resources Information Center

    Tamboer, Peter; Scholte, H. Steven; Vorst, Harrie C. M.

    2015-01-01

    In voxel-based morphometry studies of dyslexia, the relation between causal theories of dyslexia and gray matter (GM) and white matter (WM) volume alterations is still under debate. Some alterations are consistently reported, but others failed to reach significance. We investigated GM alterations in a large sample of Dutch students (37 dyslexics…

  9. [Roentgen morphometry of the shoulder in diseased rotator cuff. Value of plain roentgen examination in comparison with arthroscopy].

    PubMed

    Gerber, B; Hempfling, H

    1995-02-01

    A comparison between the pathomorphological substrate and the X-ray morphometry of the shoulder joint was made with 482 arthroscopically treated patients. Radiological parameters and indices for the prediction of the development of the impingement-syndrome were developed from this comparison. With these parameters and indices is it possible to predict the pathomorphological substrate and to differentiate between subacromial and coracoidal impingement.

  10. In Vivo Lung Morphometry With Hyperpolarized 3He Diffusion MRI: Reproducibility and the Role of Diffusion Sensitizing Gradient Direction

    PubMed Central

    Quirk, James D.; Chang, Yulin V.; Yablonskiy, Dmitriy A.

    2014-01-01

    Purpose Lung morphometry with hyperpolarized gas diffusion MRI is a highly sensitive technique for the non-invasive measurement of acinar microstructural parameters traditionally only accessible by histology. The goal of this work is to establish the reproducibility of these measurements in healthy volunteers and their dependence upon the direction of the applied diffusion-sensitizing gradient. Methods Helium-3 lung morphometry MRI was performed on a total of five healthy subjects. Two subjects received duplicate imaging on the same day and three after a four or twenty-seven month delay to assess reproducibility. Four subjects repeated the measurement during the same session with different diffusion-sensitizing gradient directions to determine the effect on the parameter estimates. Results The helium-3 lung morphometry measurements were reproducible over the short and long term (e.g. % coefficient of variation (CV) of mean chord length, Lm = 2.1% and 2.9% respectively) and across different diffusion gradient directions (Lm % CV = 2.6%). Results also show independence of field inhomogeneity effects at 1.5T. Conclusion Helium-3 lung morphometry is a reproducible technique for measuring acinar microstructure and is effectively independent of the choice of diffusion gradient direction. This provides confidence for the use of this technique to compare populations and treatment efficacy. PMID:24752926

  11. Assessing the effects of iron enrichment across holobiont compartments reveals reduced microbial nitrogen fixation in the Red Sea coral Pocillopora verrucosa.

    PubMed

    Rädecker, Nils; Pogoreutz, Claudia; Ziegler, Maren; Ashok, Ananya; Barreto, Marcelle M; Chaidez, Veronica; Grupstra, Carsten G B; Ng, Yi Mei; Perna, Gabriela; Aranda, Manuel; Voolstra, Christian R

    2017-08-01

    The productivity of coral reefs in oligotrophic tropical waters is sustained by an efficient uptake and recycling of nutrients. In reef-building corals, the engineers of these ecosystems, this nutrient recycling is facilitated by a constant exchange of nutrients between the animal host and endosymbiotic photosynthetic dinoflagellates (zooxanthellae), bacteria, and other microbes. Due to the complex interactions in this so-called coral holobiont, it has proven difficult to understand the environmental limitations of productivity in corals. Among others, the micronutrient iron has been proposed to limit primary productivity due to its essential role in photosynthesis and bacterial processes. Here, we tested the effect of iron enrichment on the physiology of the coral Pocillopora verrucosa from the central Red Sea during a 12-day experiment. Contrary to previous reports, we did not see an increase in zooxanthellae population density or gross photosynthesis. Conversely, respiration rates were significantly increased, and microbial nitrogen fixation was significantly decreased. Taken together, our data suggest that iron is not a limiting factor of primary productivity in Red Sea corals. Rather, increased metabolic demands in response to iron enrichment, as evidenced by increased respiration rates, may reduce carbon (i.e., energy) availability in the coral holobiont, resulting in reduced microbial nitrogen fixation. This decrease in nitrogen supply in turn may exacerbate the limitation of other nutrients, creating a negative feedback loop. Thereby, our results highlight that the effects of iron enrichment appear to be strongly dependent on local environmental conditions and ultimately may depend on the availability of other nutrients.

  12. In vivo two-photon imaging reveals a role of progesterone in reducing axonal dieback after spinal cord injury in mice.

    PubMed

    Yang, Zhijie; Xie, Wenguang; Ju, Furong; Khan, Akbar; Zhang, Shengxiang

    2017-04-01

    Progesterone (PG) as a neuroprotective reagent has been used for the treatment of spinal cord injury (SCI) in experimental animal models. However, its effect and mechanism on axonal dieback at the early stage of SCI remain unclear. Here, we investigate the dynamics of injured axons and the effect of PG on the axonal dieback, glial response, and behavioral recovery in a mouse model of SCI. Two-photon intravital imaging combined with a simplified imaging window chamber were used to image axons in hemisected spinal cords over a period of 3 days. Repeated imaging showed that axonal dieback distance in mice treated with PG after SCI was significantly reduced than that in mice treated with vehicle after SCI (P < 0.05) at the time point of 24 h, 48 h, and 72 h after SCI. The densities of astrocytes and microglia in the SCI-vehicle treated group were significantly higher than those in mice treated with PG after SCI (P < 0.05). Real time polymerase chain reaction assay indicated that administration of PG after SCI down-regulated the expression of pro-inflammatory cytokines MCP-1, NOS2, and IL-1β (P < 0.05). PG treatment also improved the behavioral performance post injury. These findings suggested that PG exerted a neuroprotective effect by attenuating axonal dieback, reducing the accumulation of astrocytes and microglia and inhibiting the release of pro-inflammatory cytokines.

  13. Bacterial communities in haloalkaliphilic sulfate-reducing bioreactors under different electron donors revealed by 16S rRNA MiSeq sequencing.

    PubMed

    Zhou, Jiemin; Zhou, Xuemei; Li, Yuguang; Xing, Jianmin

    2015-09-15

    Biological technology used to treat flue gas is useful to replace conventional treatment, but there is sulfide inhibition. However, no sulfide toxicity effect was observed in haloalkaliphilic bioreactors. The performance of the ethanol-fed bioreactor was better than that of lactate-, glucose-, and formate-fed bioreactor, respectively. To support this result strongly, Illumina MiSeq paired-end sequencing of 16S rRNA gene was applied to investigate the bacterial communities. A total of 389,971 effective sequences were obtained and all of them were assigned to 10,220 operational taxonomic units (OTUs) at a 97% similarity. Bacterial communities in the glucose-fed bioreactor showed the greatest richness and evenness. The highest relative abundance of sulfate-reducing bacteria (SRB) was found in the ethanol-fed bioreactor, which can explain why the performance of the ethanol-fed bioreactor was the best. Different types of SRB, sulfur-oxidizing bacteria, and sulfur-reducing bacteria were detected, indicating that sulfur may be cycled among these microorganisms. Because high-throughput 16S rRNA gene paired-end sequencing has improved resolution of bacterial community analysis, many rare microorganisms were detected, such as Halanaerobium, Halothiobacillus, Desulfonatronum, Syntrophobacter, and Fusibacter. 16S rRNA gene sequencing of these bacteria would provide more functional and phylogenetic information about the bacterial communities. Copyright © 2015 Elsevier B.V. All rights reserved.

  14. A Voxel-Based Morphometry Study Reveals Local Brain Structural Alterations Associated with Ambient Fine Particles in Older Women

    PubMed Central

    Casanova, Ramon; Wang, Xinhui; Reyes, Jeanette; Akita, Yasuyuki; Serre, Marc L.; Vizuete, William; Chui, Helena C.; Driscoll, Ira; Resnick, Susan M.; Espeland, Mark A.; Chen, Jiu-Chiuan

    2016-01-01

    Objective: Exposure to ambient fine particulate matter (PM2.5: PM with aerodynamic diameters < 2.5 μm) has been linked with cognitive deficits in older adults. Using fine-grained voxel-wise analyses, we examined whether PM2.5 exposure also affects brain structure. Methods: Brain MRI data were obtained from 1365 women (aged 71–89) in the Women's Health Initiative Memory Study and local brain volumes were estimated using RAVENS (regional analysis of volumes in normalized space). Based on geocoded residential locations and air monitoring data from the U.S. Environmental Protection Agency, we employed a spatiotemporal model to estimate long-term (3-year average) exposure to ambient PM2.5 preceding MRI scans. Voxel-wise linear regression models were fit separately to gray matter (GM) and white matter (WM) maps to analyze associations between brain structure and PM2.5 exposure, with adjustment for potential confounders. Results: Increased PM2.5 exposure was associated with smaller volumes in both cortical GM and subcortical WM areas. For GM, associations were clustered in the bilateral superior, middle, and medial frontal gyri. For WM, the largest clusters were in the frontal lobe, with smaller clusters in the temporal, parietal, and occipital lobes. No statistically significant associations were observed between PM2.5 exposure and hippocampal volumes. Conclusions: Long-term PM2.5 exposures may accelerate loss of both GM and WM in older women. While our previous work linked smaller WM volumes to PM2.5, this is the first neuroimaging study reporting associations between air pollution exposure and smaller volumes of cortical GM. Our data support the hypothesized synaptic neurotoxicity of airborne particles. PMID:27790103

  15. Effects of Hormone Therapy on Brain Volumes Changes of Postmenopausal Women Revealed by Optimally-Discriminative Voxel-Based Morphometry.

    PubMed

    Zhang, Tianhao; Casanova, Ramon; Resnick, Susan M; Manson, JoAnn E; Baker, Laura D; Padual, Claudia B; Kuller, Lewis H; Bryan, R Nick; Espeland, Mark A; Davatzikos, Christos

    2016-01-01

    The Women's Health Initiative Memory Study Magnetic Resonance Imaging (WHIMS-MRI) provides an opportunity to evaluate how menopausal hormone therapy (HT) affects the structure of older women's brains. Our earlier work based on region of interest (ROI) analysis demonstrated potential structural changes underlying adverse effects of HT on cognition. However, the ROI-based analysis is limited in statistical power and precision, and cannot provide fine-grained mapping of whole-brain changes. We aimed to identify local structural differences between HT and placebo groups from WHIMS-MRI in a whole-brain refined level, by using a novel method, named Optimally-Discriminative Voxel-Based Analysis (ODVBA). ODVBA is a recently proposed imaging pattern analysis approach for group comparisons utilizing a spatially adaptive analysis scheme to accurately locate areas of group differences, thereby providing superior sensitivity and specificity to detect the structural brain changes over conventional methods. Women assigned to HT treatments had significant Gray Matter (GM) losses compared to the placebo groups in the anterior cingulate and the adjacent medial frontal gyrus, and the orbitofrontal cortex, which persisted after multiple comparison corrections. There were no regions where HT was significantly associated with larger volumes compared to placebo, although a trend of marginal significance was found in the posterior cingulate cortical area. The CEE-Alone and CEE+MPA groups, although compared with different placebo controls, demonstrated similar effects according to the spatial patterns of structural changes. HT had adverse effects on GM volumes and risk for cognitive impairment and dementia in older women. These findings advanced our understanding of the neurobiological underpinnings of HT effects.

  16. A Voxel-Based Morphometry Study Reveals Local Brain Structural Alterations Associated with Ambient Fine Particles in Older Women.

    PubMed

    Casanova, Ramon; Wang, Xinhui; Reyes, Jeanette; Akita, Yasuyuki; Serre, Marc L; Vizuete, William; Chui, Helena C; Driscoll, Ira; Resnick, Susan M; Espeland, Mark A; Chen, Jiu-Chiuan

    2016-01-01

    Objective: Exposure to ambient fine particulate matter (PM2.5: PM with aerodynamic diameters < 2.5 μm) has been linked with cognitive deficits in older adults. Using fine-grained voxel-wise analyses, we examined whether PM2.5 exposure also affects brain structure. Methods: Brain MRI data were obtained from 1365 women (aged 71-89) in the Women's Health Initiative Memory Study and local brain volumes were estimated using RAVENS (regional analysis of volumes in normalized space). Based on geocoded residential locations and air monitoring data from the U.S. Environmental Protection Agency, we employed a spatiotemporal model to estimate long-term (3-year average) exposure to ambient PM2.5 preceding MRI scans. Voxel-wise linear regression models were fit separately to gray matter (GM) and white matter (WM) maps to analyze associations between brain structure and PM2.5 exposure, with adjustment for potential confounders. Results: Increased PM2.5 exposure was associated with smaller volumes in both cortical GM and subcortical WM areas. For GM, associations were clustered in the bilateral superior, middle, and medial frontal gyri. For WM, the largest clusters were in the frontal lobe, with smaller clusters in the temporal, parietal, and occipital lobes. No statistically significant associations were observed between PM2.5 exposure and hippocampal volumes. Conclusions: Long-term PM2.5 exposures may accelerate loss of both GM and WM in older women. While our previous work linked smaller WM volumes to PM2.5, this is the first neuroimaging study reporting associations between air pollution exposure and smaller volumes of cortical GM. Our data support the hypothesized synaptic neurotoxicity of airborne particles.

  17. Effects of Hormone Therapy on Brain Volumes Changes of Postmenopausal Women Revealed by Optimally-Discriminative Voxel-Based Morphometry

    PubMed Central

    Zhang, Tianhao; Casanova, Ramon; Resnick, Susan M.; Manson, JoAnn E.; Baker, Laura D.; Padual, Claudia B.; Kuller, Lewis H.; Bryan, R. Nick; Espeland, Mark A.; Davatzikos, Christos

    2016-01-01

    Backgrounds The Women's Health Initiative Memory Study Magnetic Resonance Imaging (WHIMS-MRI) provides an opportunity to evaluate how menopausal hormone therapy (HT) affects the structure of older women’s brains. Our earlier work based on region of interest (ROI) analysis demonstrated potential structural changes underlying adverse effects of HT on cognition. However, the ROI-based analysis is limited in statistical power and precision, and cannot provide fine-grained mapping of whole-brain changes. Methods We aimed to identify local structural differences between HT and placebo groups from WHIMS-MRI in a whole-brain refined level, by using a novel method, named Optimally-Discriminative Voxel-Based Analysis (ODVBA). ODVBA is a recently proposed imaging pattern analysis approach for group comparisons utilizing a spatially adaptive analysis scheme to accurately locate areas of group differences, thereby providing superior sensitivity and specificity to detect the structural brain changes over conventional methods. Results Women assigned to HT treatments had significant Gray Matter (GM) losses compared to the placebo groups in the anterior cingulate and the adjacent medial frontal gyrus, and the orbitofrontal cortex, which persisted after multiple comparison corrections. There were no regions where HT was significantly associated with larger volumes compared to placebo, although a trend of marginal significance was found in the posterior cingulate cortical area. The CEE-Alone and CEE+MPA groups, although compared with different placebo controls, demonstrated similar effects according to the spatial patterns of structural changes. Conclusions HT had adverse effects on GM volumes and risk for cognitive impairment and dementia in older women. These findings advanced our understanding of the neurobiological underpinnings of HT effects. PMID:26974440

  18. Quantification and Comparison of Anti-Fibrotic Therapies by Polarized SRM and SHG-Based Morphometry in Rat UUO Model

    PubMed Central

    Weldon, Steve M.; Matera, Damian; Lee, ChungWein; Yang, Haichun; Fryer, Ryan M.; Fogo, Agnes B.; Reinhart, Glenn A.

    2016-01-01

    Renal interstitial fibrosis (IF) is an important pathologic manifestation of disease progression in a variety of chronic kidney diseases (CKD). However, the quantitative and reproducible analysis of IF remains a challenge, especially in experimental animal models of progressive IF. In this study, we compare traditional polarized Sirius Red morphometry (SRM) to novel Second Harmonic Generation (SHG)-based morphometry of unstained tissues for quantitative analysis of IF in the rat 5 day unilateral ureteral obstruction (UUO) model. To validate the specificity of SHG for detecting fibrillar collagen components in IF, co-localization studies for collagens type I, III, and IV were performed using IHC. In addition, we examined the correlation, dynamic range, sensitivity, and ability of polarized SRM and SHG-based morphometry to detect an anti-fibrotic effect of three different treatment regimens. Comparisons were made across three separate studies in which animals were treated with three mechanistically distinct pharmacologic agents: enalapril (ENA, 15, 30, 60 mg/kg), mycophenolate mofetil (MMF, 2, 20 mg/kg) or the connective tissue growth factor (CTGF) neutralizing antibody, EX75606 (1, 3, 10 mg/kg). Our results demonstrate a strong co-localization of the SHG signal with fibrillar collagens I and III but not non-fibrillar collagen IV. Quantitative IF, calculated as percent cortical area of fibrosis, demonstrated similar response profile for both polarized SRM and SHG-based morphometry. The two methodologies exhibited a strong correlation across all three pharmacology studies (r2 = 0.89–0.96). However, compared with polarized SRM, SHG-based morphometry delivered a greater dynamic range and absolute magnitude of reduction of IF after treatment. In summary, we demonstrate that SHG-based morphometry in unstained kidney tissues is comparable to polarized SRM for quantitation of fibrillar collagens, but with an enhanced sensitivity to detect treatment-induced reductions in

  19. Boron-Doped Diamond Microelectrodes Reveal Reduced Serotonin Uptake Rates in Lymphocytes from Adult Rhesus Monkeys Carrying the Short Allele of the 5-HTTLPR

    PubMed Central

    2009-01-01

    Uptake resolved by high-speed chronoamperometry on a second-by-second basis has revealed important differences in brain serotonin transporter function associated with genetic variability. Here, we use chronoamperometry to investigate variations in serotonin transport in primary lymphocytes associated with the rhesus serotonin transporter gene-linked polymorphism (rh5-HTTLPR), a promoter polymorphism whose orthologues occur only in higher order primates including humans. Serotonin clearance by lymphocytes is Na+-dependent and inhibited by the serotonin-selective reuptake inhibitor paroxetine (Paxil), indicative of active uptake by serotonin transporters. Moreover, reductions in serotonin uptake rates are evident in lymphocytes from monkeys with one or two copies of the short ‘s’ allele of the rh5-HTTLPR (s/s < s/l < l/l). These findings illustrate that rh5-HTTLPR-related alterations in serotonin uptake are present during adulthood in peripheral blood cells natively expressing serotonin transporters. Moreover, they suggest that lymphocytes can be used as peripheral biomarkers for investigating genetic or pharmacologic alterations in serotonin transporter function. Use of boron-doped diamond microelectrodes for measuring serotonin uptake, in contrast to carbon fiber microelectrodes used previously in the brain, enabled these high-sensitivity and high-resolution measurements. Boron-doped diamond microelectrodes show excellent signal-to-noise and signal-to-background ratios due mainly to low background currents and are highly resistant to fouling when exposed to lymphocytes or high concentrations of serotonin. PMID:20352073

  20. Interventions to Reduce Spasticity and Improve Function in People With Chronic Incomplete Spinal Cord Injury: Distinctions Revealed by Different Analytical Methods.

    PubMed

    Duffell, Lynsey D; Brown, Geoffrey L; Mirbagheri, Mehdi M

    2015-07-01

    Spinal cord injury (SCI) results in impaired function, and ankle joint spasticity is a common secondary complication. Different interventions have been trialed with variable results. We investigated the effects of pharmacological and physical (locomotor training) interventions on function in people living with incomplete motor function loss caused by SCI and used different analytical techniques to understand whether functional levels affect recovery with different interventions. Participants with an incomplete SCI were assigned to 3 groups: no intervention, Lokomat, or tizanidine. Outcome measures were the 10-m walk test, 6-minute walk test, and the Timed Up and Go. Participants were classified in 2 ways: (1) based on achieving an improvement above the minimally important difference (MID) and (2) using growth mixture modeling (GMM). Functional levels of participants who achieved the MID were compared and random coefficient regression (RCR) was used to assess recovery in GMM classes. Overall, walking speed and endurance improved, with no difference between interventions. Only a small number of participants achieved the MID. Both MID and GMM-RCR analyses revealed that tizanidine improved endurance in high-functioning participants. GMM-RCR classification also showed that speed and mobility improved after locomotor training. Improvements in function were achieved in a limited number of people with SCI. Using the MID and GMM techniques, differences in responses to interventions between high-and low-functioning participants could be identified. These techniques may, therefore, have potential to be used for characterizing therapeutic effects resulting from different interventions. © The Author(s) 2014.

  1. Microarray Analysis Reveals Increased Transcriptional Repression and Reduced Metabolic Activity but Not Major Changes in the Core Apoptotic Machinery during Maturation of Sympathetic Neurons.

    PubMed

    Raba, Mikk; Palgi, Jaan; Lehtivaara, Maria; Arumäe, Urmas

    2016-01-01

    Postnatal maturation of the neurons whose main phenotype and basic synaptic contacts are already established includes neuronal growth, refinement of synaptic contacts, final steps of differentiation, programmed cell death period (PCD) etc. In the sympathetic neurons, postnatal maturation includes permanent end of the PCD that occurs with the same time schedule in vivo and in vitro suggesting that the process could be genetically determined. Also many other changes in the neuronal maturation could be permanent and thus based on stable changes in the genome expression. However, postnatal maturation of the neurons is poorly studied. Here we compared the gene expression profiles of immature and mature sympathetic neurons using Affymetrix microarray assay. We found 1310 significantly up-regulated and 1151 significantly down-regulated genes in the mature neurons. Gene ontology analysis reveals up-regulation of genes related to neuronal differentiation, chromatin and epigenetic changes, extracellular factors and their receptors, and cell adhesion, whereas many down-regulated genes were related to metabolic and biosynthetic processes. We show that termination of PCD is not related to major changes in the expression of classical genes for apoptosis or cell survival. Our dataset is deposited to the ArrayExpress database and is a valuable source to select candidate genes in the studies of neuronal maturation. As an example, we studied the changes in the expression of selected genes Igf2bp3, Coro1A, Zfp57, Dcx, and Apaf1 in the young and mature sympathetic ganglia by quantitative PCR and show that these were strongly downregulated in the mature ganglia.

  2. Microarray Analysis Reveals Increased Transcriptional Repression and Reduced Metabolic Activity but Not Major Changes in the Core Apoptotic Machinery during Maturation of Sympathetic Neurons

    PubMed Central

    Raba, Mikk; Palgi, Jaan; Lehtivaara, Maria; Arumäe, Urmas

    2016-01-01

    Postnatal maturation of the neurons whose main phenotype and basic synaptic contacts are already established includes neuronal growth, refinement of synaptic contacts, final steps of differentiation, programmed cell death period (PCD) etc. In the sympathetic neurons, postnatal maturation includes permanent end of the PCD that occurs with the same time schedule in vivo and in vitro suggesting that the process could be genetically determined. Also many other changes in the neuronal maturation could be permanent and thus based on stable changes in the genome expression. However, postnatal maturation of the neurons is poorly studied. Here we compared the gene expression profiles of immature and mature sympathetic neurons using Affymetrix microarray assay. We found 1310 significantly up-regulated and 1151 significantly down-regulated genes in the mature neurons. Gene ontology analysis reveals up-regulation of genes related to neuronal differentiation, chromatin and epigenetic changes, extracellular factors and their receptors, and cell adhesion, whereas many down-regulated genes were related to metabolic and biosynthetic processes. We show that termination of PCD is not related to major changes in the expression of classical genes for apoptosis or cell survival. Our dataset is deposited to the ArrayExpress database and is a valuable source to select candidate genes in the studies of neuronal maturation. As an example, we studied the changes in the expression of selected genes Igf2bp3, Coro1A, Zfp57, Dcx, and Apaf1 in the young and mature sympathetic ganglia by quantitative PCR and show that these were strongly downregulated in the mature ganglia. PMID:27013977

  3. Preferential interactions between ApoE-containing lipoproteins and Aβ revealed by a detection method that combines size exclusion chromatography with non-reducing gel-shift.

    PubMed

    LaDu, Mary Jo; Munson, Gregory W; Jungbauer, Lisa; Getz, Godfrey S; Reardon, Catherine A; Tai, Leon M; Yu, Chunjiang

    2012-02-01

    The association between apolipoprotein E (apoE) and amyloid-β peptide (Aβ) may significantly impact the function of both proteins, thus affecting the etiology of Alzheimer's disease (AD). However, apoE/Aβ interactions remain fundamentally defined by the stringency of the detection method. Here we use size exclusion chromatography (SEC) as a non-stringent approach to the detection of apoE/Aβ interactions in solution, specifically apoE and both endogenous and exogenous Aβ from plasma, CSF and astrocyte conditioned media. By SEC analysis, Aβ association with plasma and CNS lipoproteins is apoE-dependent. While endogenous Aβ elutes to specific human plasma lipoproteins distinct from those containing apoE, it is the apoE-containing lipoproteins that absorb excess amounts of exogenous Aβ40. In human CSF, apoE, endogenous Aβ and phospholipid elute in an almost identical profile, as do apoE, exogenous Aβ and phospholipid from astrocyte conditioned media. Combining SEC fractionation with subsequent analysis for SDS-stable apoE/Aβ complex reveals that apoE-containing astrocyte lipoproteins exhibit the most robust interactions with Aβ. Thus, standardization of the methods for detecting apoE/Aβ complex is necessary to determine its functional significance in the neuropathology characteristic of AD. Importantly, a systematic understanding of the role of apoE-containing plasma and CNS lipoproteins in Aβ homeostasis could potentially contribute to identifying a plasma biomarker currently over-looked because it has multiple components. Copyright © 2011 Elsevier B.V. All rights reserved.

  4. Preferential Interactions between ApoE-containing Lipoproteins and Aβ Revealed by a Detection Method that Combines Size Exclusion Chromatography with Non-Reducing Gel-shift

    PubMed Central

    LaDu, Mary Jo; Munson, Gregory W.; Jungbauer, Lisa; Getz, Godfrey S.; Reardon, Catherine A.; Tai, Leon M.; Yu, Chunjiang

    2012-01-01

    The association between apolipoprotein E (apoE) and amyloid-β peptide (Aβ) may significantly impact the function of both proteins, thus affecting the etiology of Alzheimer’s disease (AD). However, apoE/Aβ interactions remain fundamentally defined by the stringency of the detection method. Here we use size exclusion chromatography (SEC) as a non-stringent approach to the detection of apoE/Aβ interactions in solution, specifically apoE and both endogenous and exogenous Aβ from plasma, CSF and astrocyte conditioned media. By SEC analysis, Aβ association with plasma and CNS lipoproteins is apoE-dependent. While endogenous Aβ elutes to specific human plasma lipoproteins distinct from those containing apoE, it is the apoE-containing lipoproteins that absorb excess amounts of exogenous Aβ40. In human CSF, apoE, endogenous Aβ and phospholipid elute in an almost identical profile, as do apoE, exogenous Aβ and phospholipid from astrocyte conditioned media. Combining SEC fractionation with subsequent analysis for SDS-stable apoE/Aβ complex reveals that apoE-containing astrocyte lipoproteins exhibit the most robust interactions with Aβ. Thus, standardization of the methods for detecting apoE/Aβ complex is necessary to determine its functional significance in the neuropathology characteristic of AD. Importantly, a systematic understanding of the role of apoE-containing plasma and CNS lipoproteins in Aβ homeostasis could potentially contribute to identifying a plasma biomarker currently over-looked because it has multiple components. PMID:22138302

  5. The draft genome of the hyperthermophilic archaeon Pyrodictium delaneyi strain hulk, an iron and nitrate reducer, reveals the capacity for sulfate reduction.

    PubMed

    Demey, Lucas M; Miller, Caitlin R; Manzella, Michael P; Spurbeck, Rachel R; Sandhu, Sukhinder K; Reguera, Gemma; Kashefi, Kazem

    2017-01-01

    Pyrodictium delaneyi strain Hulk is a newly sequenced strain isolated from chimney samples collected from the Hulk sulfide mound on the main Endeavour Segment of the Juan de Fuca Ridge (47.9501 latitude, -129.0970 longitude, depth 2200 m) in the Northeast Pacific Ocean. The draft genome of strain Hulk shared 99.77% similarity with the complete genome of the type strain Su06(T), which shares with strain Hulk the ability to reduce iron and nitrate for respiration. The annotation of the genome of strain Hulk identified genes for the reduction of several sulfur-containing electron acceptors, an unsuspected respiratory capability in this species that was experimentally confirmed for strain Hulk. This makes P. delaneyi strain Hulk the first hyperthermophilic archaeon known to gain energy for growth by reduction of iron, nitrate, and sulfur-containing electron acceptors. Here we present the most notable features of the genome of P. delaneyi strain Hulk and identify genes encoding proteins critical to its respiratory versatility at high temperatures. The description presented here corresponds to a draft genome sequence containing 2,042,801 bp in 9 contigs, 2019 protein-coding genes, 53 RNA genes, and 1365 hypothetical genes.

  6. Treatment with Tacrolimus and Sirolimus Reveals No Additional Adverse Effects on Human Islets In Vitro Compared to Each Drug Alone but They Are Reduced by Adding Glucocorticoids

    PubMed Central

    Kloster-Jensen, Kristine; Sahraoui, Afaf; Vethe, Nils Tore; Korsgren, Olle; Bergan, Stein; Foss, Aksel; Scholz, Hanne

    2016-01-01

    Tacrolimus and sirolimus are important immunosuppressive drugs used in human islet transplantation; however, they are linked to detrimental effects on islets and reduction of long-term graft function. Few studies investigate the direct effects of these drugs combined in parallel with single drug exposure. Human islets were treated with or without tacrolimus (30 μg/L), sirolimus (30 μg/L), or a combination thereof for 24 hrs. Islet function as well as apoptosis was assessed by glucose-stimulated insulin secretion (GSIS) and Cell Death ELISA. Proinflammatory cytokines were analysed by qRT-PCR and Bio-Plex. Islets exposed to the combination of sirolimus and tacrolimus were treated with or without methylprednisolone (1000 μg/L) and the expression of the proinflammatory cytokines was investigated. We found the following: (i) No additive reduction in function and viability in islets existed when tacrolimus and sirolimus were combined compared to the single drug. (ii) Increased expression of proinflammatory cytokines mRNA and protein levels in islets took place. (iii) Methylprednisolone significantly decreased the proinflammatory response in islets induced by the drug combination. Although human islets are prone to direct toxic effect of tacrolimus and sirolimus, we found no additive effects of the drug combination. Short-term exposure of glucocorticoids could effectively reduce the proinflammatory response in human islets induced by the combination of tacrolimus and sirolimus. PMID:26885529

  7. Volumetric and voxel-based morphometry findings in autism subjects with and without macrocephaly.

    PubMed

    Bigler, Erin D; Abildskov, Tracy J; Petrie, Jo Ann; Johnson, Michael; Lange, Nicholas; Chipman, Jonathan; Lu, Jeffrey; McMahon, William; Lainhart, Janet E

    2010-01-01

    This study sought to replicate Herbert et al. (2003a), which found increased overall white matter (WM) volume in subjects with autism, even after controlling for head size differences. To avoid the possibility that greater WM volume in autism is merely an epiphenomena of macrocephaly overrepresentation associated with the disorder, the current study included control subjects with benign macrocephaly. The control group also included subjects with a reading disability to insure cognitive heterogeneity. WM volume in autism was significantly larger, even when controlling for brain volume, rate of macrocephaly, and other demographic variables. Autism and controls differed little on whole-brain WM voxel-based morphometry (VBM) analyses suggesting that the overall increase in WM volume was non-localized. Autism subjects exhibited a differential pattern of IQ relationships with brain volumetry findings from controls. Current theories of brain overgrowth and their importance in the development of autism are discussed in the context of these findings.

  8. Vorhersage des Krankheitsverlaufes von leichten kognitiven Beeinträchtigungen durch automatisierte MRT Morphometrie

    NASA Astrophysics Data System (ADS)

    Fritzsche, Klaus H.; Schlindwein, Sarah; Stieltjes, Bram; Essig, Marco; Meinzer, Hans-Peter

    Die leichte kognitive Beeinträchtigung (LKB) gilt als Anzeichen für ein erhöhtes Risiko der Entwicklung einer Alzheimerdemenz. Eine fundierte klinische Prognose für den Krankheitsverlauf kann aber bis dato nicht gegeben werden. Das Ziel dieser Arbeit besteht darin, eine möglichst präzise Vorhersage mittels automatisierter Morphometrie des Hippokampus im MRT-Bild zu treffen. In einer Studie mit 18 Probanden mit LKB wurde eine Prädiktionsgenauigkeit für die Entwicklung einer späteren Demenz von 83.3% erzielt. Eine manuelle Vergleichsmethode erreichte mit 55.6% Trefferquote keine signifikante Vorhersagegenauigkeit. Das automatische Verfahren erfüllt viele wichtige Voraussetzungen für den routinemäßigen klinischen Einsatz mit dem Potential, die klinische Vorhersage des Krankheitsverlaufes bei der LKB zu verbessern.

  9. [Principles of voxel-based morphometry and availability of integrated software BAAD].

    PubMed

    Shiino, Akihiko

    2013-01-01

    BAAD is integrated software for investigation of brain morphological change using statistical parametric mapping (SPM). The basic part of the software is voxel-based morphometry (VBM) that has been developed by Drs. Ashburner and Friston. Pathological changes with neuronal loss results in brain atrophy, which can be detected by MRI. VBM provides an automated and unbiased assessment of such morphometric change throughout the brain. Recently, VBM has been drastically improved by introducing the Diffeomorphic Anatomical Registration Through Exponentiated Lie algebra (DARTEL) registration method that implements a high dimensional warping process. BAAD supports the full-length steps for VBM analysis and makes it easy for everyone. BAAD is a free software and works on 64bit Windows machine without MATLAB installation.

  10. Selective reduction in amygdala volume in pediatric anxiety disorders: a voxel-based morphometry investigation.

    PubMed

    Milham, Michael P; Nugent, Allison C; Drevets, Wayne C; Dickstein, Daniel P; Leibenluft, Ellen; Ernst, Monique; Charney, Dennis; Pine, Daniel S

    2005-05-01

    Significant controversy has emerged concerning pediatric anxiety disorders. Some researchers question the justification for diagnosing and treating pediatric anxiety disorders, owing to concerns about the inappropriate medicalization of social problems. Others note the importance of diagnosis and treatment, given that pediatric anxiety disorders represent a strong risk factor for serious adult mental disorders. We examine the neural correlates of pediatric anxiety disorders, to consider the validity of the categorization scheme used in recent treatment studies. Using inclusion criteria derived from recent treatment trials, we compared gray matter volume throughout the brain in children with and without anxiety. Morphometric analyses used optimized voxel-based morphometry, an automated method for examining structural changes throughout the brain. Reductions in left amygdala gray matter volume were noted for patients with anxiety disorders relative to comparison subjects. We discuss implications of these findings for current controversies.

  11. Do manual and voxel-based morphometry measure the same? A proof of concept study.

    PubMed

    Focke, Niels K; Trost, Sarah; Paulus, Walter; Falkai, Peter; Gruber, Oliver

    2014-01-01

    Voxel-based morphometry (VBM) is a commonly used method to study volumetric variations on a whole brain basis. However, it is often criticized for potential confounds, mainly based on imperfect spatial registration. We therefore aimed to evaluate if VBM and "gold standard" manual volumetry are measuring the same effects with respect to subcortical gray matter volumes. Manual regions-of-interest were drawn in the hippocampus, amygdala, nucleus accumbens, thalamus, putamen, pallidum, and caudate nucleus bilaterally. Resulting volumes were used for a whole brain VBM correlation analysis with Statistical Parametric Mapping (SPM8). The hippocampus, amygdala, putamen, and caudate nucleus were correctly identified by SPM using the contemporary high-dimensional normalization (DARTEL toolbox). This strongly suggests that VBM and manual volumetry both are indeed measuring the same effects with regard to subcortical brain structures.

  12. Evaluation of Pre-Malignant and Malignant Lesions in Cervico Vaginal (PAP) Smears by Nuclear Morphometry

    PubMed Central

    Rani M.N, Divya; Kumar ML, Harendra; SR, Sheela

    2014-01-01

    Background: Cervical cancer is the second most common cancer occurring among women worldwide, with almost half a million new cases each year. Normal cells gradually transform to form cancer cells through several stages. So, the changes occurring during the transformational stages need to be assessed. Aim: Our aim was to study various nuclear parameters useful in evaluating pre-malignant and malignant cervico-vaginal pap smears. Materials and Methods: Bethesda System was used to categorize cervical pap smears into premalignant and malignant lesions. Nuclear parameters were calculated using J 1.44C morphometric software. Several nuclear size parameters were analysed. Results: The nuclear area, perimeter, diameter were found to be statistically significant (p<0.05) parameters in differentiating premalignant from malignant cervical smears. Conclusion: Nuclear morphometry was thus a useful objective tool in differentiating premalignant from malignant cervical smears. PMID:25584229

  13. Volumetric and Voxel-Based Morphometry Findings in Autism Subjects With and Without Macrocephaly

    PubMed Central

    Bigler, Erin D.; Abildskov, Tracy J.; Petrie, Jo Ann; Johnson, Michael; Lange, Nicholas; Chipman, Jonathan; Lu, Jeffrey; McMahon, William; Lainhart, Janet E.

    2015-01-01

    This study sought to replicate Herbert et al. (2003a), which found increased overall white matter (WM) volume in subjects with autism, even after controlling for head size differences. To avoid the possibility that greater WM volume in autism is merely an epiphenomena of macrocephaly over-representation associated with the disorder, the current study included control subjects with benign macrocephaly. The control group also included subjects with a reading disability to insure cognitive heterogeneity. WM volume in autism was significantly larger, even when controlling for brain volume, rate of macrocephaly, and other demographic variables. Autism and controls differed little on whole-brain WM voxel-based morphometry (VBM) analyses suggesting that the overall increase in WM volume was non-localized. Autism subjects exhibited a differential pattern of IQ relationships with brain volumetry findings from controls. Current theories of brain overgrowth and their importance in the development of autism are discussed in the context of these findings. PMID:20446133

  14. Gray matter correlates of dispositional optimism: a voxel-based morphometry study.

    PubMed

    Yang, Junyi; Wei, Dongtao; Wang, Kangcheng; Qiu, Jiang

    2013-10-11

    Dispositional optimism is an important product of human evolution. This individual difference variable plays a core role in human experience. Dispositional optimism is beneficial to physical and psychological wellbeing. Previous task-related neuroimaging studies on dispositional optimism were limited by small sample sizes, and did not examine individual differences in dispositional optimism related to brain structure. Thus, the current study used voxel-based morphometry and the revised Life Orientation Test to investigate individual dispositional optimism and its association with brain structure in 361 healthy participants. The results showed that individual dispositional optimism was associated with larger gray matter volume of a cluster of areas that included the left thalamus/left pulvinar that extended to the left parahippocampal gyrus. These findings suggest a biological basis for individual dispositional optimism, distributed across different gray matter regions of the brain. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

  15. Voxel-based morphometry predicts shifts in dendritic spine density and morphology with auditory fear conditioning.

    PubMed

    Keifer, O P; Hurt, R C; Gutman, D A; Keilholz, S D; Gourley, S L; Ressler, K J

    2015-07-07

    Neuroimaging has provided compelling data about the brain. Yet the underlying mechanisms of many neuroimaging techniques have not been elucidated. Here we report a voxel-based morphometry (VBM) study of Thy1-YFP mice following auditory fear conditioning complemented by confocal microscopy analysis of cortical thickness, neuronal morphometric features and nuclei size/density. Significant VBM results included the nuclei of the amygdala, the insula and the auditory cortex. There were no significant VBM changes in a control brain area. Focusing on the auditory cortex, confocal analysis showed that fear conditioning led to a significantly increased density of shorter and wider dendritic spines, while there were no spine differences in the control area. Of all the morphology metrics studied, the spine density was the only one to show significant correlation with the VBM signal. These data demonstrate that learning-induced structural changes detected by VBM may be partially explained by increases in dendritic spine density.

  16. Voxel based morphometry in optical coherence tomography: validation and core findings

    NASA Astrophysics Data System (ADS)

    Antony, Bhavna J.; Chen, Min; Carass, Aaron; Jedynak, Bruno M.; Al-Louzi, Omar; Solomon, Sharon D.; Saidha, Shiv; Calabresi, Peter A.; Prince, Jerry L.

    2016-03-01

    Optical coherence tomography (OCT) of the human retina is now becoming established as an important modality for the detection and tracking of various ocular diseases. Voxel based morphometry (VBM) is a long standing neuroimaging analysis technique that allows for the exploration of the regional differences in the brain. There has been limited work done in developing registration based methods for OCT, which has hampered the advancement of VBM analyses in OCT based population studies. Following on from our recent development of an OCT registration method, we explore the potential benefits of VBM analysis in cohorts of healthy controls (HCs) and multiple sclerosis (MS) patients. Specifically, we validate the stability of VBM analysis in two pools of HCs showing no significant difference between the two populations. Additionally, we also present a retrospective study of age and sex matched HCs and relapsing remitting MS patients, demonstrating results consistent with the reported literature while providing insight into the retinal changes associated with this MS subtype.

  17. Membrane Disordering by Eicosapentaenoic Acid in B Lymphomas Is Reduced by Elongation to Docosapentaenoic Acid as Revealed with Solid-State Nuclear Magnetic Resonance Spectroscopy of Model Membranes.

    PubMed

    Harris, Mitchell; Kinnun, Jacob J; Kosaraju, Rasagna; Leng, Xiaoling; Wassall, Stephen R; Shaikh, Saame Raza

    2016-07-01

    Plasma membrane organization is a mechanistic target of n-3 (ω-3) polyunsaturated fatty acids. Previous studies show that eicosapentaenoic acid (EPA; 20:5n-3) and docosahexaenoic acid (DHA; 22:6n-3) differentially disrupt plasma membrane molecular order to enhance the frequency and function of B lymphocytes. However, it is not known whether EPA and DHA affect the plasma membrane organization of B lymphomas differently to influence their function. We tested whether EPA and DHA had different effects on membrane order in B lymphomas and liposomes and studied their effects on B-lymphoma growth. B lymphomas were treated with 25 μmol EPA, DHA, or serum albumin control/L for 24 h. Membrane order was measured with fluorescence polarization, and cellular fatty acids (FAs) were analyzed with GC. Growth was quantified with a viability assay. (2)H nuclear magnetic resonance (NMR) studies were conducted on deuterated phospholipid bilayers. Treating Raji, Ramos, and RPMI lymphomas for 24 h with 25 μmol EPA or DHA/L lowered plasma membrane order by 10-40% relative to the control. There were no differences between EPA and DHA on membrane order for the 3 cell lines. FA analyses revealed complex changes in response to EPA or DHA treatment and a large fraction of EPA was converted to docosapentaenoic acid (DPA; 22:5n-3). NMR studies, which were used to understand why EPA and DHA had similiar membrane effects, showed that phospholipids containing DPA, similar to DHA, were more ordered than those containing EPA. Finally, treating B lymphomas with 25 μmol EPA or DHA/L did not increase the frequency of B lymphomas compared with controls. The results establish that 25 μmol EPA and DHA/L equally disrupt membrane order and do not promote B lymphoma growth. The data open a new area of investigation, which is how EPA's conversion to DPA substantially moderates its influence on membrane properties. © 2016 American Society for Nutrition.

  18. Analysis of the Genome and Mobilome of a Dissimilatory Arsenate Reducing Aeromonas sp. O23A Reveals Multiple Mechanisms for Heavy Metal Resistance and Metabolism.

    PubMed

    Uhrynowski, Witold; Decewicz, Przemyslaw; Dziewit, Lukasz; Radlinska, Monika; Krawczyk, Pawel S; Lipinski, Leszek; Adamska, Dorota; Drewniak, Lukasz

    2017-01-01

    Aeromonas spp. are among the most ubiquitous microorganisms, as they have been isolated from different environmental niches including waters, soil, as well as wounds and digestive tracts of poikilothermic animals and humans. Although much attention has been paid to the pathogenicity of Aeromonads, the role of these bacteria in environmentally important processes, such as transformation of heavy metals, remains to be discovered. Therefore, the aim of this study was a detailed genomic characterization of Aeromonas sp. O23A, the first representative of this genus capable of dissimilatory arsenate reduction. The strain was isolated from microbial mats from the Zloty Stok mine (SW Poland), an environment strongly contaminated with arsenic. Previous physiological studies indicated that O23A may be involved in both mobilization and immobilization of this metalloid in the environment. To discover the molecular basis of the mechanisms behind the observed abilities, the genome of O23A (∼5.0 Mbp) was sequenced and annotated, and genes for arsenic respiration, heavy metal resistance (hmr) and other phenotypic traits, including siderophore production, were identified. The functionality of the indicated gene modules was assessed in a series of minimal inhibitory concentration analyses for various metals and metalloids, as well as mineral dissolution experiments. Interestingly, comparative analyses revealed that O23A is related to a fish pathogen Aeromonas salmonicida subsp. salmonicida A449 which, however, does not carry genes for arsenic respiration. This indicates that the dissimilatory arsenate reduction ability may have been lost during genome reduction in pathogenic strains, or acquired through horizontal gene transfer. Therefore, particular emphasis was placed upon the mobilome of O23A, consisting of four plasmids, a phage, and numerous transposable elements, which may play a role in the dissemination of hmr and arsenic metabolism genes in the environment. The obtained

  19. Bovine Teat Microbiome Analysis Revealed Reduced Alpha Diversity and Significant Changes in Taxonomic Profiles in Quarters with a History of Mastitis

    PubMed Central

    Falentin, Hélène; Rault, Lucie; Nicolas, Aurélie; Bouchard, Damien S.; Lassalas, Jacques; Lamberton, Philippe; Aubry, Jean-Marc; Marnet, Pierre-Guy; Le Loir, Yves; Even, Sergine

    2016-01-01

    Mastitis is a mammary gland inflammatory disease often due to bacterial infections. Like many other infections, it used to be considered as a host-pathogen interaction driven by host and bacterial determinants. Until now, the involvement of the bovine mammary gland microbiota in the host-pathogen interaction has been poorly investigated, and mainly during the infectious episode. In this study, the bovine teat microbiome was investigated in 31 quarters corresponding to 27 animals, which were all free of inflammation at sampling time but which had different histories regarding mastitis: from no episode of mastitis on all the previous lactations (Healthy quarter, Hq) to one or several clinical mastitis events (Mastitic quarter, Mq). Several quarters whose status was unclear (possible history of subclinical mastitis) were classified as NDq. Total bacterial DNA was extracted from foremilk samples and swab samples of the teat canal. Taxonomic profiles were determined by pyrosequencing on 16s amplicons of the V3-4 region. Hq quarters showed a higher diversity compared to Mq ones (Shannon index: ~8 and 6, respectively). Clustering of the quarters based on their bacterial composition made it possible to separate Mq and Hq quarters into two separate clusters (C1 and C2, respectively). Discriminant analysis of taxonomic profiles between these clusters revealed several differences and allowed the identification of taxonomic markers in relation to mastitis history. C2 quarters were associated with a higher proportion of the Clostridia class (including genera such as Ruminococcus, Oscillospira, Roseburia, Dorea, etc.), the Bacteroidetes phylum (Prevotella, Bacteroides, Paludibacter, etc.), and the Bifidobacteriales order (Bifidobacterium), whereas C1 quarters showed a higher proportion of the Bacilli class (Staphylococcus) and Chlamydiia class. These results indicate that microbiota is altered in udders which have already developed mastitis, even far from the infectious episode

  20. Analysis of gene expression pattern reveals potential targets of dietary oleoylethanolamide in reducing body fat gain in C3H mice.

    PubMed

    Thabuis, Clémentine; Destaillats, Frédéric; Landrier, Jean-François; Tissot-Favre, Delphine; Martin, Jean-Charles

    2010-10-01

    Oleoylethanolamide (OEA) has been previously reported to regulate food intake and body weight gain when administered intraperitoneally. Nevertheless, little information is available with regard to oral administration. To assess whether oral OEA can also exert a similar effect on body fat, we fed C3H mice a high-fat diet supplemented with either 10 or 100 mg/kg body weight OEA for 4 weeks. OEA supplementation significantly lowered food intake over the 4 weeks and decreased adipose tissue mass. Plasma triglyceride levels were also significantly decreased by OEA treatment. In order to identify the potential molecular targets of OEA action, we screened the expression levels of 44 genes related to body fat mass and food intake in peripheral tissues. Adipose tissue fatty acid amide hydrolase (FAAH), intestinal fatty acid transporter/cluster of differentiation 36 and the OEA receptor G-protein-coupled receptor 119 (GPR119) were among the most OEA-responsive genes. They were also associated with reduced body fat pads regardless of the dose. Adipose FAAH was found to be primarily associated with a decrease in food intake. Our data suggest that the anti-obesity activity of OEA partially relies on modulation of the FAAH pathway in adipose tissue. Another mechanism might involve modulation of the newly discovered GPR119 OEA signaling pathway in the proximal intestine. In conclusion, our study indicates that oral administration of OEA can effectively decrease obesity in the mouse model and that modulation of the endocannabinoid fatty acid ethanolamide pathway seems to play an important role both in adipose tissue and in small intestine. Copyright © 2010 Elsevier Inc. All rights reserved.

  1. Spatio-temporal dynamics of sulfate-reducing bacteria in extreme environment of Rogoznica Lake revealed by 16S rRNA analysis

    NASA Astrophysics Data System (ADS)

    Čanković, Milan; Petrić, Ines; Marguš, Marija; Ciglenečki, Irena

    2017-08-01

    Highly eutrophic and euxinic seawater system of Rogoznica Lake (Croatia) was used as a study site for investigation of distribution, diversity and abundance of sulfate-reducing bacteria (SRB) during stratified conditions in the summer and winter season, by targeting 6 phylogenetic subgroups of SRB. 16S rRNA gene sequences indicated that community cannot be directly related to cultured SRB species but rather that Rogoznica Lake harbors habitat-specific SRB populations associated to bacteria belonging to δ-Proteobacteria with few Firmicutes and Verrucomicrobium-related populations. Clear spatial-temporal shifts in the SRB community structure were observed. Results implied existence of distinct SRB populations between the water column and sediment, as well as higher diversity of the SRB occupying water layer then the ones found in the sediment. Likewise, seasonal variations in populations were observed. While SRB community was more diverse in the winter compared to the summer season in the water layer, situation was opposite in the sediment. Water layer communities seem to be more susceptible to changes of physico-chemical parameters, while those in the sediment have prorogated response to these changes. Results indicate that SRB diversity is still highly underestimated in natural environments, especially in specific habitats such as Rogoznica Lake. Presented data show a complex SRB diversity and distribution supporting the idea that habitat-specific SRB communities are important part of the anaerobic food chain in degradation of organic matter as well as cycling of sulfur and carbon species in the Lake and similar anoxic environment.

  2. When the brain goes diving: transcriptome analysis reveals a reduced aerobic energy metabolism and increased stress proteins in the seal brain.

    PubMed

    Fabrizius, Andrej; Hoff, Mariana Leivas Müller; Engler, Gerhard; Folkow, Lars P; Burmester, Thorsten

    2016-08-09

    During long dives, the brain of whales and seals experiences a reduced supply of oxygen (hypoxia). The brain neurons of the hooded seal (Cystophora cristata) are more tolerant towards low-oxygen conditions than those of mice, and also better survive other hypoxia-related stress conditions like a reduction in glucose supply and high concentrations of lactate. Little is known about the molecular mechanisms that support the hypoxia tolerance of the diving brain. Here we employed RNA-seq to approach the molecular basis of the unusual stress tolerance of the seal brain. An Illumina-generated transcriptome of the visual cortex of the hooded seal was compared with that of the ferret (Mustela putorius furo), which served as a terrestrial relative. Gene ontology analyses showed a significant enrichment of transcripts related to translation and aerobic energy production in the ferret but not in the seal brain. Clusterin, an extracellular chaperone, is the most highly expressed gene in the seal brain and fourfold higher than in the ferret or any other mammalian brain transcriptome. The largest difference was found for S100B, a calcium-binding stress protein with pleiotropic function, which was 38-fold enriched in the seal brain. Notably, significant enrichment of S100B mRNA was also found in the transcriptomes of whale brains, but not in the brains of terrestrial mammals. Comparative transcriptomics indicates a lower aerobic capacity of the seal brain, which may be interpreted as a general energy saving strategy. Elevated expression of stress-related genes, such as clusterin and S100B, possibly contributes to the remarkable hypoxia tolerance of the brain of the hooded seal. Moreover, high levels of S100B that possibly protect the brain appear to be the result of the convergent adaptation of diving mammals.

  3. Metaproteogenomic analysis of a sulfate-reducing enrichment culture reveals genomic organization of key enzymes in the m-xylene degradation pathway and metabolic activity of proteobacteria.

    PubMed

    Bozinovski, Dragana; Taubert, Martin; Kleinsteuber, Sabine; Richnow, Hans-Hermann; von Bergen, Martin; Vogt, Carsten; Seifert, Jana

    2014-10-01

    This study aimed to ascertain the functional and phylogenetic relationships within an m-xylene degrading sulfate-reducing enrichment culture, which had been maintained for several years in the laboratory with m-xylene as the sole source of carbon and energy. Previous studies indicated that a phylotype affiliated to the Desulfobacteraceae was the main m-xylene assimilating organism. In the present study, genes and gene products were identified by a metaproteogenomic approach using LC-MS/MS analysis of the microbial community, and 2426 peptides were identified from 576 proteins. In the metagenome of the community, gene clusters encoding enzymes involved in fumarate addition to a methyl moiety of m-xylene (nms, bss), as well as gene clusters coding for enzymes involved in modified beta-oxidation to (3-methyl)benzoyl-CoA (bns), were identified in two separate contigs. Additionally, gene clusters containing homologues to bam genes encoding benzoyl-CoA reductase (Bcr) class II, catalyzing the dearomatization of (3-methyl)benzoyl-CoA, were identified. Time-resolved protein stable isotope probing (protein-SIP) experiments using (13)C-labeled m-xylene showed that the respective gene products were highly (13)C-labeled. The present data suggested the identification of gene products that were similar to those involved in methylnaphthalene degradation even though the consortium was not capable of growing in the presence of naphthalene, methylnaphthalene or toluene as substrates. Thus, a novel branch of enzymes was found that was probably specific for anaerobic m-xylene degradation. Copyright © 2014 Elsevier GmbH. All rights reserved.

  4. Absence of Cu-Zn superoxide dismutase BCSOD1 reduces Botrytis cinerea virulence in Arabidopsis and tomato plants, revealing interplay among reactive oxygen species, callose and signalling pathways.

    PubMed

    López-Cruz, Jaime; Óscar, Crespo-Salvador; Emma, Fernández-Crespo; Pilar, García-Agustín; Carmen, González-Bosch

    2017-01-01

    Plants activate responses against pathogens, including the oxidative burst. Necrotrophic pathogens can produce reactive oxygen species (ROS) that benefit the colonization process. Previously, we have demonstrated that tomato plants challenged with Botrytis cinerea accumulate ROS and callose, together with the induction of genes involved in defence, signalling and oxidative metabolism. Here, we studied the infection phenotype of the Δbcsod1 strain in both tomato and Arabidopsis plants. This mutant lacks bcsod1, which encodes Cu-Zn superoxide dismutase (SOD). This enzyme catalyses the conversion of superoxide ion ( O2-) into hydrogen peroxide (H2 O2 ). ROS play a protective role and act as signals in plants. Δbcsod1 displayed reduced virulence compared with wild-type B05.10 in both species. Plants infected with Δbcsod1 accumulated less H2 O2 and more O2- than those infected with B05.10, which is associated with an increase in the defensive polymer callose. This supports a major role of fungal SOD in H2 O2 production during the plant-pathogen interaction. The early induction of the callose synthase gene PMR4 suggested that changes in ROS altered plant defensive responses at the transcriptional level. The metabolites and genes involved in signalling and in response to oxidative stress were differentially expressed on Δbcsod1 infection, supporting the notion that plants perceive changes in ROS balance and activate defence responses. A higher O2(-) /H2 O2 ratio seems to be beneficial for plant protection against this necrotroph. Our results highlight the relevance of callose and the oxylipin 12-oxo-phytodienoic acid (OPDA) in the response to changes in the oxidative environment, and clarify the mechanisms that underlie the responses to Botrytis in Arabidopsis and tomato plants. © 2016 BSPP and John Wiley & Sons Ltd.

  5. Prefrontal cortex morphometry in abstinent adolescent marijuana users: Subtle gender effects

    PubMed Central

    Medina, Krista Lisdahl; McQueeny, Tim; Nagel, Bonnie J.; Hanson, Karen L.; Yang, Tony T.; Tapert, Susan F.

    2009-01-01

    Introduction Adult human studies suggest frontal dysfunction associated with chronic marijuana (MJ) use, but due to continued neuromaturation, adult studies may not generalize to adolescents. This study characterized prefrontal cortex (PFC) morphometry in chronic MJ-using adolescents following one month of monitored abstinence. Methods Data were collected from MJ users (n=16) and controls (n=16) aged 16-18. Extensive exclusionary criteria included comorbid psychiatric and neurologic disorders. Substance use and anatomical measures were collected after 28 days of monitored abstinence. PFC volumes were ascertained from manual tracing by reliable raters on high-resolution magnetic resonance images. Results After controlling for lifetime alcohol use, gender, and intracranial volume, MJ users did not differ from controls in PFC volume. However, marginal group-by-gender interactions were observed (p<.09): female MJ users demonstrated comparatively larger PFC volumes while male MJ users had smaller volumes compared to same-gender controls. Further, group status and total PFC volume interacted in predicting executive functioning (p<.05). Among MJ users, smaller PFC total volume was associated with better executive functioning while the opposite pattern was seen among the controls. Conclusions These preliminary results indicate that gender may moderate the relationship between MJ use and PFC morphometry. Given the relationship between larger PFC total volumes and poorer executive functioning among MJ users, female MJ users may be at increased risk for neurocognitive consequences. Future research will measure PFC gray and white matter separately and follow boys and girls over adolescence to examine the influence of MJ use on neurodevelopment. PMID:19650817

  6. Taxonomic Identity of the Invasive Fruit Fly Pest, Bactrocera invadens: Concordance in Morphometry and DNA Barcoding

    PubMed Central

    Khamis, Fathiya M.; Masiga, Daniel K.; Mohamed, Samira A.; Salifu, Daisy; de Meyer, Marc; Ekesi, Sunday

    2012-01-01

    In 2003, a new fruit fly pest species was recorded for the first time in Kenya and has subsequently been found in 28 countries across tropical Africa. The insect was described as Bactrocera invadens, due to its rapid invasion of the African continent. In this study, the morphometry and DNA Barcoding of different populations of B. invadens distributed across the species range of tropical Africa and a sample from the pest's putative aboriginal home of Sri Lanka was investigated. Morphometry using wing veins and tibia length was used to separate B. invadens populations from other closely related Bactrocera species. The Principal component analysis yielded 15 components which correspond to the 15 morphometric measurements. The first two principal axes contributed to 90.7% of the total variance and showed partial separation of these populations. Canonical discriminant analysis indicated that only the first five canonical variates were statistically significant. The first two canonical variates contributed a total of 80.9% of the total variance clustering B. invadens with other members of the B. dorsalis complex while distinctly separating B. correcta, B. cucurbitae, B. oleae and B. zonata. The largest Mahalanobis squared distance (D2 = 122.9) was found to be between B. cucurbitae and B. zonata, while the lowest was observed between B. invadens populations against B. kandiensis (8.1) and against B. dorsalis s.s (11.4). Evolutionary history inferred by the Neighbor-Joining method clustered the Bactrocera species populations into four clusters. First cluster consisted of the B. dorsalis complex (B. invadens, B. kandiensis and B. dorsalis s. s.), branching from the same node while the second group was paraphyletic clades of B. correcta and B. zonata. The last two are monophyletic clades, consisting of B. cucurbitae and B. oleae, respectively. Principal component analysis using the genetic distances confirmed the clustering inferred by the NJ tree. PMID:23028649

  7. Influence of staining and sampling procedures on goat sperm morphometry using the Sperm Class Analyzer.

    PubMed

    Hidalgo, Manuel; Rodríguez, Inmaculada; Dorado, Jesús

    2006-09-01

    Computer-assisted sperm morphometry analysis (ASMA) has improved the assessment of sperm morphology, but the results depend on the use of adequate sampling and staining procedures of spermatozoa from individual species. In this study, the Sperm Class Analyzer ASMA system was used for the morphometric analysis of goat sperm heads. Semen samples, obtained from four bucks, were used to evaluate the influence of three staining procedures (Diff-Quik, Hemacolor and Harris' Haematoxylin) on the accuracy of image processing and sperm morphometry, the effect of the number of cells analysed and the repeatability of the method. These experiments were performed to obtain objective, accurate and reliable sperm morphometric measurements of goat spermatozoa. Diff-Quik and Harris' Haematoxylin were significantly (p<0.05) more accurate than Hemacolor. However, Diff-Quik obtained the highest proportion of correctly analysed sperm heads (86.06%) and the lowest coefficients of variation on the image processing and morphometric measurements. The staining methods affected significantly the sperm dimensions (p<0.001) with increased values from Diff-Quik than Hemacolor and Harris' Haematoxylin, respectively (Diff-Quik>Hemacolor>Harris' Haematoxylin). No differences in morphometric parameters were found when 100, 150, 175 or 200 spermatozoa were analysed. The repeatability of results obtained was very high since no differences were found when measuring the same sperm on multiple attempts. In conclusion, to obtain objective, accurate and repeatable sperm morphometric measurements by the Sperm Class Analyzer system in goats, the analysis of 100 spermatozoa from slides which have been previously stained with Diff-Quik is recommended.

  8. APPLYING TENSOR-BASED MORPHOMETRY TO PARAMETRIC SURFACES CAN IMPROVE MRI-BASED DISEASE DIAGNOSIS

    PubMed Central

    Wang, Yalin; Yuan, Lei; Shi, Jie; Greve, Alexander; Ye, Jieping; Toga, Arthur W.; Reiss, Allan L.; Thompson, Paul M.

    2013-01-01

    Many methods have been proposed for computer-assisted diagnostic classification. Full tensor information and machine learning with 3D maps derived from brain images may help detect subtle differences or classify subjects into different groups. Here we develop a new approach to apply tensor-based morphometry to parametric surface models for diagnostic classification. We use this approach to identify cortical surface features for use in diagnostic classifiers. First, with holomorphic 1-forms, we compute an efficient and accurate conformal mapping from a multiply connected mesh to the so-called slit domain. Next, the surface parameterization approach provides a natural way to register anatomical surfaces across subjects using a constrained harmonic map. To analyze anatomical differences, we then analyze the full Riemannian surface metric tensors, which retain multivariate information on local surface geometry. As the number of voxels in a 3D image is large, sparse learning is a promising method to select a subset of imaging features and to improve classification accuracy. Focusing on vertices with greatest effect sizes, we train a diagnostic classifier using the surface features selected by an ℓ1-norm based sparse learning method. Stability selection is applied to validate the selected feature sets. We tested the algorithm on MRI-derived cortical surfaces from 42 subjects with genetically confirmed Williams syndrome and 40 age-matched controls, multivariate statistics on the local tensors gave greater effect sizes for detecting group differences relative to other TBM-based statistics including analysis of the Jacobian determinant and the largest eigenvalue of the surface metric. Our method also gave reasonable classification results relative to the Jacobian determinant, the pair of eigenvalues of the Jacobian matrix and volume features. This analysis pipeline may boost the power of morphometry studies, and may assist with image-based classification. PMID:23435208

  9. Negative and interactive effects of sex, aging, and alcohol abuse on gray matter morphometry.

    PubMed

    Thayer, Rachel E; Hagerty, Sarah L; Sabbineni, Amithrupa; Claus, Eric D; Hutchison, Kent E; Weiland, Barbara J

    2016-06-01

    Chronic alcohol use is associated with declines in gray matter (GM) volume, as is the normal aging process. Less apparent, however, is how the interaction between aging and heavy alcohol use affects changes in GM across the lifespan. There is some evidence that women are more vulnerable to the negative effects of alcohol use on GM than men. In the current study, we examined whether localized GM was related to measures of alcohol use disorder (e.g., AUDIT score) in a large sample (N = 436) of participants, ages 18-55 years, with a range of disease severity, using both voxel-based morphometry (VBM) and surface-based morphometry (SBM). We also explored whether GM associations with alcohol use disorder (AUD) severity are moderated by sex and age. Results showed significant negative associations between AUD severity and GM volume throughout temporal, parietal, frontal, and occipital lobes. Women showed more negative effects of alcohol use than men for cortical thickness in left orbitofrontal cortex, but evidence for increased vulnerability based on sex was limited overall. Similarly, a specific age by alcohol use interaction was observed for volume of right insula, but other regional or global interactions were not statistically supported. However, significant negative associations between heavy alcohol use and GM volumes were observed as early as 18-25 years. These findings support that alcohol has deleterious effects on global and regional GM above and beyond age, and, of particular importance, that regional associations emerge in early adulthood. Hum Brain Mapp 37:2276-2292, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  10. Negative and Interactive Effects of Sex, Aging, and Alcohol Abuse on Gray Matter Morphometry

    PubMed Central

    Thayer, Rachel E.; Hagerty, Sarah L.; Sabbineni, Amithrupa; Claus, Eric D.; Hutchison, Kent E.; Weiland, Barbara J.

    2016-01-01

    Chronic alcohol use is associated with declines in gray matter volume, as is the normal aging process. Less apparent, however, is how the interaction between aging and heavy alcohol use affects changes in gray matter across the lifespan. There is some evidence that women are more vulnerable to the negative effects of alcohol use on gray matter than men. In the current study, we examined whether localized gray matter was related to measures of alcohol use disorder (e.g., AUDIT score) in a large sample (N = 436) of participants, ages 18–55 years, with a range of disease severity, using both voxel-based morphometry (VBM) and surface-based morphometry (SBM). We also explored whether gray matter associations with alcohol use disorder (AUD) severity are moderated by sex and age. Results showed significant negative associations between AUD severity and gray matter volume throughout temporal, parietal, frontal, and occipital lobes. Women showed more negative effects of alcohol use than men for cortical thickness in left orbitofrontal cortex, but evidence for increased vulnerability based on sex was limited overall. Similarly, a specific age by alcohol use interaction was observed for volume of right insula, but other regional or global interactions were not statistically supported. However, significant negative associations between heavy alcohol use and gray matter volumes were observed as early as 18–25 years. These findings support that alcohol has deleterious effects on global and regional gray matter above and beyond age, and, of particular importance, that regional associations emerge in early adulthood. PMID:26947584

  11. Aging-related changes in respiratory system mechanics and morphometry in mice.

    PubMed

    Elliott, Jonathan E; Mantilla, Carlos B; Pabelick, Christina M; Roden, Anja C; Sieck, Gary C

    2016-07-01

    Previous work investigating respiratory system mechanics in mice has reported an aging-related increase in compliance and mean linear intercept (Lm). However, these changes were assessed using only a young (2-mo-old) and old (20- and 26-mo-old) group yet were interpreted to reflect a linear evolution across the life span. Therefore, to investigate respiratory system mechanics and lung morphometry across a more complete spectrum of ages, we utilized 2 (100% survival, n = 6)-, 6 (100% survival, n = 12)-, 18 (90% survival, n = 12)-, 24 (75% survival, n = 12)-, and 30 (25% survival, n = 12)-mo-old C57BL/6 mice. We found a nonlinear aging-related decrease in respiratory system resistance and increase in dynamic compliance and hysteresis between 2- and 24-mo-old mice. However, in 30-mo-old mice, respiratory system resistance increased, and dynamic compliance and hysteresis decreased relative to 24-mo-old mice. Respiratory system impedance spectra were measured between 1-20.5 Hz at positive end-expiratory pressures (PEEP) of 1, 3, 5, and 7 cmH2O. Respiratory system resistance and reactance at each level of PEEP were increased and decreased, respectively, only in 2-mo-old animals. No differences in the respiratory system impedance spectra were observed in 6-, 18-, 24-, and 30-mo-old mice. Additionally, lungs were fixed following tracheal instillation of 4% paraformaldehyde at 25 cmH2O and processed for Lm and airway collagen deposition. There was an aging-related increase in Lm consistent with emphysematous-like changes and no evidence of increased airway collagen deposition. Accordingly, we demonstrate nonlinear aging-related changes in lung mechanics and morphometry in C57BL/6 mice.

  12. Reproducibility of Brain Morphometry from Short-Term Repeat Clinical MRI Examinations: A Retrospective Study

    PubMed Central

    Liu, Hon-Man; Chen, Shan-Kai; Chen, Ya-Fang; Lee, Chung-Wei; Yeh, Lee-Ren

    2016-01-01

    Purpose To assess the inter session reproducibility of automatic segmented MRI-derived measures by FreeSurfer in a group of subjects with normal-appearing MR images. Materials and Methods After retrospectively reviewing a brain MRI database from our institute consisting of 14,758 adults, those subjects who had repeat scans and had no history of neurodegenerative disorders were selected for morphometry analysis using FreeSurfer. A total of 34 subjects were grouped by MRI scanner model. After automatic segmentation using FreeSurfer, label-wise comparison (involving area, thickness, and volume) was performed on all segmented results. An intraclass correlation coefficient was used to estimate the agreement between sessions. Wilcoxon signed rank test was used to assess the population mean rank differences across sessions. Mean-difference analysis was used to evaluate the difference intervals across scanners. Absolute percent difference was used to estimate the reproducibility errors across the MRI models. Kruskal-Wallis test was used to determine the across-scanner effect. Results The agreement in segmentation results for area, volume, and thickness measurements of all segmented anatomical labels was generally higher in Signa Excite and Verio models when compared with Sonata and TrioTim models. There were significant rank differences found across sessions in some labels of different measures. Smaller difference intervals in global volume measurements were noted on images acquired by Signa Excite and Verio models. For some brain regions, significant MRI model effects were observed on certain segmentation results. Conclusions Short-term scan-rescan reliability of automatic brain MRI morphometry is feasible in the clinical setting. However, since repeatability of software performance is contingent on the reproducibility of the scanner performance, the scanner performance must be calibrated before conducting such studies or before using such software for retrospective

  13. Structural brain abnormalities in borderline personality disorder: A voxel-based morphometry study

    PubMed Central

    Soloff, Paul; Nutche, Jeffrey; Goradia, Dhruman; Diwadkar, Vaibhav

    2012-01-01

    Imaging studies using ROI morphometry and PET have contributed to our understanding of structural and functional abnormalities in BPD; however, both methods have practical limitations to their usefulness for exploratory studies of brain-behavior relationships. We used voxel based morphometry (VBM) in 34 subjects with BPD and 30 healthy controls (HC) to study effects of diagnosis, gender, childhood sexual abuse, depressed mood, impulsivity and aggression on group differences. VBM is a computer-based method for whole brain analysis that combines the advantages of a functional study with a structural method. The BPD subjects, diagnosed with the Diagnostic Interview for Borderline Patients and the International Personality Disorders Examination, were compared with 30 HC, with age and gender covaried. Analyses were repeated separately by gender and, in women, by histories of childhood sexual abuse. Depressed mood, impulsivity, and aggression were covaried in separate analyses. Compared with HC, BPD subjects had significant bilateral reductions in gray matter concentrations in ventral cingulate gyrus and several regions of the medial temporal lobe, including the hippocampus, amygdala, parahippocampal gyrus, and uncus. BPD women (and abused BPD women), but not BPD men, had significant reductions in medial temporal lobe, including the amygdala. BPD men, but not BPD women, showed diminished gray matter concentrations in the anterior cingulate gyrus compared with findings HC. Covarying for depressed mood rendered group differences non-significant in the ventral cingulate but had little effect on differences in medial temporal cortex. Covarying for aggression (LHA) had relatively little effect on group differences, while covarying for impulsivity (BIS) rendered all previously noted voxel-level group differences non-significant. Diminished gray matter in the prefrontal cortex and the medial temporal cortex may mediate the dysregulation of impulse and affect in BPD. Group

  14. Fully automated corneal endothelial morphometry of images captured by clinical specular microscopy

    NASA Astrophysics Data System (ADS)

    Bucht, Curry; Söderberg, Per; Manneberg, Göran

    2010-02-01

    The corneal endothelium serves as the posterior barrier of the cornea. Factors such as clarity and refractive properties of the cornea are in direct relationship to the quality of the endothelium. The endothelial cell density is considered the most important morphological factor of the corneal endothelium. Pathological conditions and physical trauma may threaten the endothelial cell density to such an extent that the optical property of the cornea and thus clear eyesight is threatened. Diagnosis of the corneal endothelium through morphometry is an important part of several clinical applications. Morphometry of the corneal endothelium is presently carried out by semi automated analysis of pictures captured by a Clinical Specular Microscope (CSM). Because of the occasional need of operator involvement, this process can be tedious, having a negative impact on sampling size. This study was dedicated to the development and use of fully automated analysis of a very large range of images of the corneal endothelium, captured by CSM, using Fourier analysis. Software was developed in the mathematical programming language Matlab. Pictures of the corneal endothelium, captured by CSM, were read into the analysis software. The software automatically performed digital enhancement of the images, normalizing lights and contrasts. The digitally enhanced images of the corneal endothelium were Fourier transformed, using the fast Fourier transform (FFT) and stored as new images. Tools were developed and applied for identification and analysis of relevant characteristics of the Fourier transformed images. The data obtained from each Fourier transformed image was used to calculate the mean cell density of its corresponding corneal endothelium. The calculation was based on well known diffraction theory. Results in form of estimated cell density of the corneal endothelium were obtained, using fully automated analysis software on 292 images captured by CSM. The cell density obtained by the

  15. Morphometry of distal end radius in the Indian population: A radiological study

    PubMed Central

    Mishra, Pankaj Kumar; Nagar, Manoj; Gaur, Suresh Chandra; Gupta, Anuj

    2016-01-01

    Introduction: The morphometry of distal end radius (DER) comprises the four necessary parameters: radial inclination, palmer tilt, radial height, and ulnar variance. The unblemished intellect about the morphometry is urged for the management of fracture of DER. The goal of our study was to determine the values of morphometric parameters of the DER from the adult Indian. Materials and Methods: It was a single hospital- based observational cross-sectional, prospective study. Radial inclination, radial height, and ulnar variance were measured on posteroanterior view, and the measurement of palmer tilt was accomplished on the lateral view. All the statistical analysis was done by Microsoft XL 2007 (data add in function were installed for data analysis). T-test was used for comparing the means of the parameters. Results: Two hundred and forty two (n = 242) X-rays were included in this study to analyze. The mean value (n = 242) of radial inclination was 23.27°± (standard deviation [SD]) 7.42° (range: 11.3–42.1°), palmer tilt 10.07° ± (SD) 5.28° (range: 1–16.9°), radial height 11.31 mm ± (SD) 4.9 mm (range: 7.1–30.4 mm), and ulnar variance 0.66 mm ± (SD) 2.46 mm (range: −2.4 to +4.1). Conclusion: This study may provide an inauguratory plinth to prosecute the further analytical research in the Indian population. Moreover, the data may also be used as a reference data for the anatomical alignment while treating the injuries of the DER in the Indian population. PMID:27904215

  16. A terrestrial analog for transverse aeolian ridges (TARs): Environment, morphometry, and recent dynamics

    NASA Astrophysics Data System (ADS)

    Hugenholtz, Chris H.; Barchyn, Thomas E.

    2017-06-01

    Transverse aeolian ridges (TARs) are a distinct aeolian bedform found on Mars. The formative processes, evolution, and geological significance of TARs is poorly understood. Fundamentally, it is unknown whether TARs are dunes, mega-ripples, or another bedform type. We examined aeolian bedforms in the Lut Desert of Iran as a terrestrial analog for Martian TARs. From an objective sampling strategy with high-resolution satellite imagery, we developed a large morphometric dataset for comparison with existing Martian TARs. We also examined the dynamics of the Lut bedforms between 2004 and 2012 to determine if they were static or migrating. Results indicate that the range in the dimensions (length, width, height, and wavelength) of the Lut bedforms and Martian TARs overlap, suggesting Lut bedforms are a viable terrestrial TAR analog. Our sample yielded median values of 55.18 m, 9.80, 1.02 m, and 20 m for length (longest planview axis), width (shortest planview axis), height, and wavelength, respectively. Cumulative log-frequency plots of morphometric parameters suggest the sample is from a single population and process mechanism. Although the vast majority of Lut bedforms examined were static between 2004 and 2012, some migrated up to 0.09 myr-1 on average. This is much slower than nearby dunes (4-12 myr-1), but is explained by the existence of a surface lag of coarse particles on the TAR-like bedforms. The combination of morphometry, surface sedimentology, and slow migration rate indicate the Lut bedforms are mega-ripples, which provides evidence supporting interpretation of Martian TARs as mega-ripples. Testing the mega-ripple hypothesis for Martian TARs requires measurements of their sedimentology, which may be possible with the Mars Science Laboratory rover Curiosity, as well as expanded measurements of TAR morphometry to constrain their size, shape, and scaling.

  17. Multi-functionality of computer-aided quantitative vertebral fracture morphometry analyses

    PubMed Central

    Oei, Ling; Ly, Felisia; El Saddy, Salih; Makurthou, Ater A.; Hofman, Albert; van Rooij, Frank J. A.; Uitterlinden, André G.; Zillikens, M. Carola; Rivadeneira, Fernando

    2013-01-01

    Osteoporotic vertebral fractures are an increasingly active area of research. Oftentimes assessments are performed by software-assisted quantitative morphometry. Here, we will discuss multi-functionality of these data for research purposes. A team of trained research assistants processed lateral spine radiographs from the population-based Rotterdam Study with SpineAnalyzer® software (Optasia Medical Ltd, Cheadle, UK). Next, the raw coordinate data of the two upper corners of Th5 and the two lower corners of Th12 were extracted to calculate the Cobb’s kyphosis angle. In addition, two readers performed independent manual measurements of the Cobb’s kyphosis angle between Th5 and Th12 for a sample (n=99). The mean kyphosis angle and its standard deviation were 53° and 10° for the SpineAnalyzer® software measurements and 54° and 12° by manual measurements, respectively. The Pearson’s correlation coefficient was 0.65 [95% confidence interval (CI): 0.53-0.75; P=2×10–13]. There was a substantial intraclass correlation with a coefficient of 0.64 (95% CI: 0.51-0.74). The mean difference between methods was 1° (95% CI: –2°-4°), with 95% limits of agreement of –20°-17° and there were no systematic biases. In conclusion, vertebral fracture morphometry data can be used to derive the Cobb’s kyphosis angle. Even more quantitative measures could be derived from the raw data, such as vertebral wedging, intervertebral disc space, spondylolisthesis and the lordosis angle. These measures may be of interest for research into musculoskeletal disorders such as osteoporosis, degenerative disease or Scheuermann’s disease. Large-scale studies may benefit from efficient capture of multiple quantitative measures in the spine. PMID:24273742

  18. Human Spine Morphometry In The Post-Somitic Phase : Study Of 9 Embryos.

    NASA Astrophysics Data System (ADS)

    Le Floch-Prigent, Patrice P.; Mandarim de Lacerda, Carlos A.; Hureau, Jacques; Hidden, Genevieve

    1986-07-01

    The volume of the spine was measured in 9 embryos from 8 to 31 mm crown-rump length (complete series of sagittal sections). Spine morphometry was performed by planimetrical point counting of horizontal projections on a 5 mm square grid. Total spine volume was integrated by multiplication of the thickness by the area : V = t ET=1 Si. The integrated volumes (including the base of the skull around the foramen magnum) were aligned on the diagram semi-logarithmic volume v.s. linear crown-rump length. The correlation between the spine volume and the total weight of the spine is very high (r=0,94 ; p<0,01). The spine growth of the embryos during the post-somitic phase corresponds to the general laws for this period (particularly acceleration in the second half), one of the most interesting for morphometry during the uterine life. The vertebral morphology is perfecting between the two extremities of the observed period with a nearby adult disposition at 31 mm. Datation of the 9 embryos was determined from their C-R length by means of the table published by MOORE and al. (1981) from 641 staged embryos of the Carnegie Institute, thus establishing their stage with actual admitted criteria. There was no important variation of the unique spine curvature during the postsomitic phase. Linear measurements of maximal width on the entire embryos and their spine were determined from the total number of sections and those where the vertebrae could be observed. The two widths reported to crown-rump length, drew linear curvatures with a slight irregularity, emphasized by plotting the values of three indices. These variations could be dued to the imprecision in section thickness and to the individual variation during the spinal growth for this embryonic phase. In contrast with linear data, the morphometrical method applied to the spine volume has proved to be very effective in quantitative studies for embryos of the post-somitic phase.

  19. Reduced thalamic volume in men with antisocial personality disorder or schizophrenia and a history of serious violence and childhood abuse.

    PubMed

    Kumari, V; Gudjonsson, G H; Raghuvanshi, S; Barkataki, I; Taylor, P; Sumich, A; Das, K; Kuipers, E; Ffytche, D H; Das, M

    2013-05-01

    Violent behaviour has been associated with presence of certain mental disorders, most notably antisocial personality disorder (ASPD) and schizophrenia, childhood abuse, and multiple brain abnormalities. This study examined for the first time, to the authors' knowledge, the role of psychosocial deprivation (PSD), including childhood physical and sexual abuse, in structural brain volumes of violent individuals with ASPD or schizophrenia. Fifty-six men (26 with ASPD or schizophrenia and a history of serious violence, 30 non-violent) underwent magnetic resonance imaging and were assessed on PSD. Stereological volumetric brain ratings were examined for group differences and their association with PSD ratings. PSD-brain associations were examined further using voxel-based-morphometry. The findings revealed: reduced thalamic volume in psychosocially-deprived violent individuals, relative to non-deprived violent individuals and healthy controls; negative association between thalamic volume and abuse ratings (physical and sexual) in violent individuals; and trend-level negative associations between PSD and hippocampal and prefrontal volumes in non-violent individuals. The voxel-based-morphometry analysis detected a negative association between PSD and localised grey matter volumes in the left inferior frontal region across all individuals, and additionally in the left middle frontal and precentral gyri in non-violent individuals. Violent mentally-disordered individuals with PSD, relative to those with no or minimal PSD, suffer from an additional brain deficit, i.e., reduced thalamic volume; this may affect sensory information processing, and have implications for management, of these individuals. PSD may have a stronger relationship with volumetric loss of stress-linked regions, namely the frontal cortex, in non-violent individuals. Copyright © 2012 Elsevier Masson SAS. All rights reserved.

  20. Increased medial temporal lobe and striatal grey-matter volume in a rare disorder of androgen excess: a voxel-based morphometry (VBM) study

    PubMed Central

    Mueller, Sven C.; Merke, Deborah P.; Leschek, Ellen W.; Fromm, Steven; VanRyzin, Carol; Ernst, Monique

    2016-01-01

    Major questions remain about how sex hormones influence human brain development and cognition. Studies in humans and animals suggest a strong impact of androgen on the structure and function of the medial temporal lobe (MTL) and striatum. Using voxel-based morphometry (DARTEL), we compared MTL and striatal structures in 13 [mean age (±s.d.) 12.7 ± 3.2 yr, mean bone age 14.8 ± 3.2 yr] boys with familial male precocious puberty (FMPP), characterized by early excess androgen secretion, and 39 healthy age-matched boys (mean age 14.3 ± 2.5 yr). The FMPP group showed significantly larger grey-matter volume (GMV) in parahippocampal and fusiform gyri as well as putamen relative to controls. By comparison, larger GMV for controls relative to patients was only apparent in the precentral gyrus. Exploratory regression analyses that examined the impact of age on the current findings revealed a significant increase of GMV in the putamen with age in patients suffering from excess androgen but not in controls. Finally, current levels of free testosterone were obtained in the patient group. Analyses revealed a significant negative association indicating that FMPP boys with low levels of bioavailable testosterone exhibited high GMV in the bilateral striatum. The findings suggest a critical influence of androgen on human brain development and are discussed in relation to male-dominant psychiatric childhood disorders. PMID:20860880

  1. Thumbprint Terrain in Isidis Planitia, Mars: Geology, Ages, Morphology, and Morphometry

    NASA Astrophysics Data System (ADS)

    Hiesinger, H.; Rohkamp, D.; Sturm, S.; Thiessen, F.; Reiss, D.

    2009-04-01

    smaller. Our measurements of the ridge heights revealed that the median height is largest (33 m) for category III. This is similar to the heights of the longer ridges of categories IV (28 m) and V (32 m). The heights of individual cones (13 m) and small ridges with less than 4 cones (21 m) are typically smaller. These heights are comparable to various terrestrial analogues, including pingos, volcanic cones, pseudocraters, and mud volcanoes. In order to further constrain the formation process of TPT, we plotted the basal diameter of the cones against their basal diameter/crater ratio. Comparing these data to terrestrial monogenetic volcanoes [10], we find the best agreement with cinder cones and pseudocraters and to a lesser extent with maars and spatter cones. To constrain the formation age of the TPT, we performed crater counts for the geologic units and nearby rampart craters that are superposed on the TPT. Based on these crater counts, we propose that the TPT in western Isidis Planitia could have formed between approximately 2.5 and 3.0 Ga. If unit Aps [11] in the eastern part of the basin has covered the TPT that was originally exposed throughout the basin, its formation can be further constrained to about 2.7 to 3.0 Ga. On the basis of our study, we conclude that: (1) thumbprint ridges are on average less than 35 m high, but there are a few with heights up to more than 70 m; (2) the occurrence of central depressions associated with the ridges/cones is interpreted as evidence for an explosive origin (e.g., volcanic cones); (3) the basal and central depression diameters are most consistent with terrestrial cinder cones and pseudocraters and to a lesser extent with maars and spatter cones; (4) on the basis of the morphology and morphometry, other origins including various types of moraines, sand ridges, dunes, eskers, drumlins, kames, crevasse fill, beach ridges, berms, table mountains, mud volcanoes, and inverted topography are less likely; (5) TPT was formed sometimes

  2. Genetic Variation in the Catechol-O-Methyl Transferase Val108/158Met Is Linked to the Caudate and Posterior Cingulate Cortex Volume in Healthy Subjects: Voxel-Based Morphometry Analysis of Brain Magnetic Resonance Imaging

    PubMed Central

    Watanabe, Keita; Kakeda, Shingo; Yoshimura, Reiji; Ide, Satoru; Hayashi, Kenji; Katsuki, Asuka; Umene-Nakano, Wakako; Watanabe, Rieko; Abe, Osamu; Korogi, Yukunori

    2015-01-01

    The effect of the catechol-O-methyltransferase (COMT) Val158Met polymorphism on brain morphology has been investigated but remains controversial. We hypothesized that a comparison between Val/Val and Val/Met individuals, which may represent the most different combinations concerning the effects of the COMT genotype, may reveal new findings. We investigated the brain morphology using 3-Tesla magnetic resonance imaging in 27 Val/Val and 22 Val/Met individuals. Voxel-based morphometry revealed that the volumes of the bilateral caudate and posterior cingulate cortex were significantly smaller in Val/Val individuals than in Val/Met individuals [right caudate: false discovery rate (FDR)-corrected p = 0.048; left caudate: FDR-corrected p = 0.048; and bilateral posterior cingulate cortex: FDR-corrected p = 0.048]. This study demonstrates that interacting functional variants of COMT affect gray matter regional volumes in healthy subjects. PMID:26566126

  3. Voxel-based morphometry at ultra-high fields. A comparison of 7T and 3T MRI data

    PubMed Central

    Seiger, Rene; Hahn, Andreas; Hummer, Allan; Kranz, Georg S; Ganger, Sebastian; Küblböck, Martin; Kraus, Christoph; Sladky, Ronald; Kasper, Siegfried; Windischberger, Christian; Lanzenberger, Rupert

    2017-01-01

    Recent technological progress enables MRI recordings at ultra-high fields of 7 Tesla and above leading to brain images of higher resolution and increased signal-to-noise ratio. Despite these benefits, imaging at 7T exhibits distinct challenges due to B1 field inhomogeneities, causing decreased image quality and problems in data analysis. Although several strategies have been proposed, a systematic investigation of bias-corrected 7T data for voxel-based morphometry (VBM) is still missing and it is an ongoing matter of debate if VBM at 7T can be carried out properly. Here, an optimized VBM study was conducted, evaluating the impact of field strength (3T vs 7T) and pulse sequence (MPRAGE vs MP2RAGE) on gray matter volume (GMV) estimates. More specifically, twenty-two participants were measured under the conditions 3T MPRAGE, 7T MPRAGE and 7T MP2RAGE. Due to the fact that 7T MPRAGE data exhibited strong intensity inhomogeneities, an alternative preprocessing pipeline was proposed and applied for that data. VBM analysis revealed higher GMV estimates for 7T predominantly in superior cortical areas, caudate nucleus, cingulate cortex and the hippocampus. On the other hand, 3T yielded higher estimates especially in inferior cortical areas of the brain, cerebellum, thalamus and putamen compared to 7T. Besides minor exceptions, these results were observed for 7T MPRAGE as well for the 7T MP2RAGE measurements. Results gained in the inferior parts of the brain should be taken with caution, as native GM segmentations displayed misclassifications in these regions for both 7T sequences. This was supported by the test-retest measurements showing highest variability in these inferior regions of the brain for 7T also for the advanced MP2RAGE sequence. Hence, our data support the use of 7T MRI for VBM analysis in cortical areas, but direct comparison between field strengths and sequences requires careful assessment. Similarly, analysis of inferior cortical regions, cerebellum and

  4. Tissue optical clearing, three-dimensional imaging, and computer morphometry in whole mouse lungs and human airways.

    PubMed

    Scott, Gregory D; Blum, Emily D; Fryer, Allison D; Jacoby, David B

    2014-07-01

    In whole adult mouse lung, full identification of airway nerves (or other cellular/subcellular objects) has not been possible due to patchy distribution and micron-scale size. Here we describe a method using tissue clearing to acquire the first complete image of three-dimensional (3D) innervation in the lung. We then created a method to pair analysis of nerve (or any other colabeled epitope) images with identification of 3D tissue compartments and airway morphometry by using fluorescent casting and morphometry software (which we designed and are making available as open-source). We then tested our method to quantify a sparse heterogeneous nerve population by examining visceral pleural nerves. Finally, we demonstrate the utility of our method in human tissue to image full thickness innervation in irregular 3D tissue compartments and to quantify sparse objects (intrinsic airway ganglia). Overall, this method can uniquely pair the advantages of whole tissue imaging and cellular/subcellular fluorescence microscopy.

  5. Cytological Study of Breast Carcinoma Before and After Oncotherapy with Special Reference to Morphometry and Proliferative Activity.

    PubMed

    Koley, Sananda; Chakrabarti, Srabani; Pathak, Swapan; Manna, Asim Kumar; Basu, Siddhartha

    2015-12-01

    Our study was done to assess the cytological changes due to oncotherapy in breast carcinoma especially on morphometry and proliferative activity. Cytological aspirates were collected from a total of 32 cases of invasive ductal carcinoma both before and after oncotherapy. Morphometry was done on the stained cytological smears to assess the different morphological parameters of cell dimension by using the ocular morphometer and the software AutoCAD 2007. Staining was done with Ki-67 and proliferating cell nuclear antigen (PCNA) as proliferative markers. Different morphological parameters were compared before and after oncotherapy by unpaired Student's t test. Statistically significant differences were found in morphometric parameters, e.g., mean nuclear diameter, mean nuclear area, mean cell diameter, and mean cell area, and in the expression of proliferative markers (Ki-67 and PCNA). Statistical analysis was done by obtaining p values. There are statistically significant differences between morphological parameter of breast carcinoma cells before and after oncotherapy.

  6. Study of nuclear morphometry on cytology specimens of benign and malignant breast lesions: A study of 122 cases

    PubMed Central

    Kashyap, Anamika; Jain, Manjula; Shukla, Shailaja; Andley, Manoj

    2017-01-01

    Background: Breast cancer has emerged as a leading site of cancer among women in India. Fine needle aspiration cytology (FNAC) has been routinely applied in assessment of breast lesions. Cytological evaluation in breast lesions is subjective with a “gray zone” of 6.9–20%. Quantitative evaluation of nuclear size, shape, texture, and density parameters by morphometry can be of diagnostic help in breast tumor. Aims: To apply nuclear morphometry on cytological breast aspirates and assess its role in differentiating between benign and malignant breast lesions with derivation of suitable cut-off values between the two groups. Settings and Designs: The present study was a descriptive cross-sectional hospital-based study of nuclear morphometric parameters of benign and malignant cases. Materials and Methods: The study included 50 benign breast disease (BBD), 8 atypical ductal hyperplasia (ADH), and 64 carcinoma cases. Image analysis was performed on Papanicolaou-stained FNAC slides by Nikon Imaging Software (NIS)–Elements Advanced Research software (Version 4.00). Nuclear morphometric parameters analyzed included 5 nuclear size, 2 shape, 4 texture, and 2 density parameters. Results: Nuclear morphometry could differentiate between benign and malignant aspirates with a gradually increasing nuclear size parameters from BBD to ADH to carcinoma. Cut-off values of 31.93 μm2, 6.325 μm, 5.865 μm, 7.855 μm, and 21.55 μm for mean nuclear area, equivalent diameter, minimum feret, maximum ferret, and perimeter, respectively, were derived between benign and malignant cases, which could correctly classify 7 out of 8 ADH cases. Conclusion: Nuclear morphometry is a highly objective tool that could be used to supplement FNAC in differentiating benign from malignant lesions, with an important role in cases with diagnostic dilemma. PMID:28182052

  7. Study of nuclear morphometry on cytology specimens of benign and malignant breast lesions: A study of 122 cases.

    PubMed

    Kashyap, Anamika; Jain, Manjula; Shukla, Shailaja; Andley, Manoj

    2017-01-01

    Breast cancer has emerged as a leading site of cancer among women in India. Fine needle aspiration cytology (FNAC) has been routinely applied in assessment of breast lesions. Cytological evaluation in breast lesions is subjective with a "gray zone" of 6.9-20%. Quantitative evaluation of nuclear size, shape, texture, and density parameters by morphometry can be of diagnostic help in breast tumor. To apply nuclear morphometry on cytological breast aspirates and assess its role in differentiating between benign and malignant breast lesions with derivation of suitable cut-off values between the two groups. The present study was a descriptive cross-sectional hospital-based study of nuclear morphometric parameters of benign and malignant cases. The study included 50 benign breast disease (BBD), 8 atypical ductal hyperplasia (ADH), and 64 carcinoma cases. Image analysis was performed on Papanicolaou-stained FNAC slides by Nikon Imaging Software (NIS)-Elements Advanced Research software (Version 4.00). Nuclear morphometric parameters analyzed included 5 nuclear size, 2 shape, 4 texture, and 2 density parameters. Nuclear morphometry could differentiate between benign and malignant aspirates with a gradually increasing nuclear size parameters from BBD to ADH to carcinoma. Cut-off values of 31.93 μm(2), 6.325 μm, 5.865 μm, 7.855 μm, and 21.55 μm for mean nuclear area, equivalent diameter, minimum feret, maximum ferret, and perimeter, respectively, were derived between benign and malignant cases, which could correctly classify 7 out of 8 ADH cases. Nuclear morphometry is a highly objective tool that could be used to supplement FNAC in differentiating benign from malignant lesions, with an important role in cases with diagnostic dilemma.

  8. Salt sensitivity of the morphometry of Artemia franciscana during development: a demonstration of 3D critical windows.

    PubMed

    Mueller, Casey A; Willis, Eric; Burggren, Warren W

    2016-02-01

    A 3D conceptual framework of 'critical windows' was used to examine whether the morphometry of Artemia franciscana is altered by salinity exposure during certain key periods of development. Artemia franciscana were hatched at 20 ppt (designated control salinity) and were then exposed to 10, 30, 40 or 50 ppt either chronically (days 1-15) or only on days 1-6, 7-9, 10-12 or 13-15. On day 15, maturity was assessed and morphometric characteristics, including mass, total body length, tail length and width, length of the third swimming appendage and eye diameter, were measured. Maturation and morphometry on day 15 were influenced by the exposure window and salinity dose. Artemia franciscana were generally larger following exposure to 10 and 40 ppt during days 1-6 and 7-9 when compared with days 10-12 and 13-15, in part due to a higher percentage of mature individuals. Exposure to different salinities on days 1-6 produced the greatest differences in morphometry, and thus this appears to be a period in development when A. franciscana is particularly sensitive to salinity. Viewing the developmental window as three-dimensional allowed more effective visualization of the complex interactions between exposure window, stressor dose and the magnitude of morphometric changes in A. franciscana. © 2016. Published by The Company of Biologists Ltd.

  9. Comparison of DXA Scans and Conventional X-rays for Spine Morphometry and Bone Age Determination in Children.

    PubMed

    Hoyer-Kuhn, Heike; Knoop, Kai; Semler, Oliver; Kuhr, Kathrin; Hellmich, Martin; Schoenau, Eckhard; Koerber, Friederike

    2016-01-01

    Conventional lateral spine and hand radiographs are the standard tools to evaluate vertebral morphometry and bone age in children. Beside bone mineral density analyses, dual-energy X-ray absorptiometry (DXA) measurements with lower radiation exposure provide high-resolution scans which are not approved for diagnostic purposes. Data about the comparability of conventional radiographs and DXA in children are missing yet. The purpose of the trial was to evaluate whether conventional hand and spine radiographs can be replaced by DXA scans to diminish radiation exposure. Thirty-eight children with osteogenesis imperfecta or secondary osteoporosis or short stature (male, n=20; age, 5.0-17.0 yr) were included and assessed once by additional DXA (GE iDXA) of the spine or the left hand. Intraclass correlation coefficients (ICCs) were used to express agreement between X-ray and iDXA assessment. Evaluation of the spine morphometry showed reasonable agreement between iDXA and radiography (ICC for fish-shape, 0.75; for wedge-shape, 0.65; and for compression fractures, 0.70). Bone age determination showed excellent agreement between iDXA and radiography (ICC, 0.97). IDXA-scans of the spine in a pediatric population should be used not only to assess bone mineral density but also to evaluate anatomic structures and vertebral morphometry. Therefore, iDXA can replace some radiographs in children with skeletal diseases.

  10. Whole lung morphometry with 3D multiple b-value hyperpolarized gas MRI and compressed sensing.

    PubMed

    Chan, Ho-Fung; Stewart, Neil J; Parra-Robles, Juan; Collier, Guilhem J; Wild, Jim M

    2017-05-01

    To demonstrate three-dimensional (3D) multiple b-value diffusion-weighted (DW) MRI of hyperpolarized (3) He gas for whole lung morphometry with compressed sensing (CS). A fully-sampled, two b-value, 3D hyperpolarized (3) He DW-MRI dataset was acquired from the lungs of a healthy volunteer and retrospectively undersampled in the ky and kz phase-encoding directions for CS simulations. Optimal k-space undersampling patterns were determined by minimizing the mean absolute error between reconstructed and fully-sampled (3) He apparent diffusion coefficient (ADC) maps. Prospective three-fold, undersampled, 3D multiple b-value (3) He DW-MRI datasets were acquired from five healthy volunteers and one chronic obstructive pulmonary disease (COPD) patient, and the mean values of maps of ADC and mean alveolar dimension (LmD ) were validated against two-dimensional (2D) and 3D fully-sampled (3) He DW-MRI experiments. Reconstructed undersampled datasets showed no visual artifacts and good preservation of the main image features and quantitative information. A good agreement between fully-sampled and prospective undersampled datasets was found, with a mean difference of +3.4% and +5.1% observed in mean global ADC and LmD values, respectively. These differences were within the standard deviation range and consistent with values reported from healthy and COPD lungs. Accelerated CS acquisition has facilitated 3D multiple b-value (3) He DW-MRI scans in a single breath-hold, enabling whole lung morphometry mapping. Magn Reson Med 77:1916-1925, 2017. © 2016 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. © 2016 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals

  11. Divide and Conquer: Sub-Grouping of ASD Improves ASD Detection Based on Brain Morphometry

    PubMed Central

    Baum, Stefi A.; Cahill, Nathan D.; Michael, Andrew M.

    2016-01-01

    Low success (<60%) in autism spectrum disorder (ASD) classification using brain morphometry from the large multi-site ABIDE dataset and inconsistent findings on brain morphometric abnormalities in ASD can be attributed to the ASD heterogeneity. In this study, we show that ASD brain morphometry is highly heterogeneous, and demonstrate that the heterogeneity can be mitigated and classification improved if autism severity (AS), verbal IQ (VIQ) and age are used with morphometric features. Morphometric features from structural MRIs (sMRIs) of 734 males (ASD: 361, controls: 373) of ABIDE were derived using FreeSurfer. Applying the Random Forest classifier, an AUC of 0.61 was achieved. Adding VIQ and age to morphometric features, AUC improved to 0.68. Sub-grouping the subjects by AS, VIQ and age improved the classification with the highest AUC of 0.8 in the moderate-AS sub-group (AS = 7–8). Matching subjects on age and/or VIQ in each sub-group further improved the classification with the highest AUC of 0.92 in the low AS sub-group (AS = 4–5). AUC decreased with AS and VIQ, and was the lowest in the mid-age sub-group (13–18 years). The important features were mainly from the frontal, temporal, ventricular, right hippocampal and left amygdala regions. However, they highly varied with AS, VIQ and age. The curvature and folding index features from frontal, temporal, lingual and insular regions were dominant in younger subjects suggesting their importance for early detection. When the experiments were repeated using the Gradient Boosting classifier similar results were obtained. Our findings suggest that identifying brain biomarkers in sub-groups of ASD can yield more robust and insightful results than searching across the whole spectrum. Further, it may allow identification of sub-group specific brain biomarkers that are optimized for early detection and monitoring, increasing the utility of sMRI as an important tool for early detection of ASD. PMID:27065101

  12. Divide and Conquer: Sub-Grouping of ASD Improves ASD Detection Based on Brain Morphometry.

    PubMed

    Katuwal, Gajendra J; Baum, Stefi A; Cahill, Nathan D; Michael, Andrew M

    2016-01-01

    Low success (<60%) in autism spectrum disorder (ASD) classification using brain morphometry from the large multi-site ABIDE dataset and inconsistent findings on brain morphometric abnormalities in ASD can be attributed to the ASD heterogeneity. In this study, we show that ASD brain morphometry is highly heterogeneous, and demonstrate that the heterogeneity can be mitigated and classification improved if autism severity (AS), verbal IQ (VIQ) and age are used with morphometric features. Morphometric features from structural MRIs (sMRIs) of 734 males (ASD: 361, controls: 373) of ABIDE were derived using FreeSurfer. Applying the Random Forest classifier, an AUC of 0.61 was achieved. Adding VIQ and age to morphometric features, AUC improved to 0.68. Sub-grouping the subjects by AS, VIQ and age improved the classification with the highest AUC of 0.8 in the moderate-AS sub-group (AS = 7-8). Matching subjects on age and/or VIQ in each sub-group further improved the classification with the highest AUC of 0.92 in the low AS sub-group (AS = 4-5). AUC decreased with AS and VIQ, and was the lowest in the mid-age sub-group (13-18 years). The important features were mainly from the frontal, temporal, ventricular, right hippocampal and left amygdala regions. However, they highly varied with AS, VIQ and age. The curvature and folding index features from frontal, temporal, lingual and insular regions were dominant in younger subjects suggesting their importance for early detection. When the experiments were repeated using the Gradient Boosting classifier similar results were obtained. Our findings suggest that identifying brain biomarkers in sub-groups of ASD can yield more robust and insightful results than searching across the whole spectrum. Further, it may allow identification of sub-group specific brain biomarkers that are optimized for early detection and monitoring, increasing the utility of sMRI as an important tool for early detection of ASD.

  13. Experimental study of inflammatory response and collagen morphometry with different types of meshes.

    PubMed

    Maeda, C T; Artigani Neto, R; Lopes-Filho, G J; Linhares, M M

    2016-12-01

    To compare an inflammation score and collagen morphometry after incisional hernia repair with four different meshes at two time points. Four types of mesh were used to repair an abdominal wall incisional defect in Wistar rats: high-density polypropylene (HW/PP); low-density polypropylene (LW/PP); polypropylene mesh encapsulated with polydioxanone coated with oxidized cellulose (PP/CE); and expanded polytetrafluoroethylene (ePTFE). An inflammation score based on histological analysis and collagen morphometry was performed after 7 and 28 days after operation (POD). Compared to LW/PP group at 7 POD, HW/PP group had lower (p = 0.014) and PP/CE group had higher inflammation scores (p = 0.001). At 28 POD, higher scores were seen in all the other groups compared to the LW/PP group (HW/PP, p = 0.046; PP/CE, p < 0.001; ePTFE, p = 0.027). Comparing groups individually at 7 and 28 PODs, all demonstrated lower inflammation score values at 28 POD (HW/PP, p < 0.001; LW/PP, p < 0.001; PP/CE, p = 0.002; ePTFE, p = 0.001). At 7 POD, higher amounts of collagen were detected in ePTFE compared to HW/PP (p < 0.001) and LW/PP (p = 0.004) and in PPCE group compared to HW/PP (p = 0.022). At 28 POD, no statistically significant difference was found. Comparing groups individually at 7 and 28 PODs, HW/PP and LW/PP showed larger amounts of collagen at the 28th POD, without any statistically significant differences for the PP/CE and ePTFE groups. Inflammation scores decreased in all groups at 28 POD. Collagen deposition was higher for non-composite meshes at 28 POD.

  14. Gray Matter Differences between Pediatric Obsessive-Compulsive Disorder Patients and High-Risk Siblings: A Preliminary Voxel-Based Morphometry Study

    PubMed Central

    Gilbert, Andrew R.; Keshavan, Matcheri S.; Diwadkar, Vaibhav; Nutche, Jeffrey; MacMaster, Frank; Easter, Phillip C.; Buhagiar, Christian J.; Rosenberg, David R.

    2008-01-01

    Neuroimaging studies have identified alterations in frontostriatal circuitry in OCD. Voxel-based morphometry (VBM) allows for the assessment of differences in gray matter density across the whole brain. VBM has not previously been used to examine regional gray matter density in pediatric OCD patients and the siblings of pediatric OCD patients. Volumetric magnetic resonance imaging (MRI) studies were conducted in 10 psychotropic-naïve pediatric patients with OCD, 10 unaffected siblings of pediatric patients with OCD, and 10 healthy controls. VBM analysis was conducted using SPM2. Statistical comparisons were performed with the general linear model, implementing small volume random field corrections for a priori regions of interest (anterior cingulate cortex or ACC, striatum and thalamus). VBM analysis revealed significantly lower gray matter density in OCD patients compared to healthy in the left ACC and bilateral medial superior frontal gyrus (SFG). Furthermore, a small volume correction was used to identify a significantly greater gray matter density in the right putamen in OCD patients as compared to unaffected siblings of OCD patients. These findings in patients, siblings, and healthy controls, although preliminary, suggest the presence of gray matter structural differences between affected subjects and healthy controls as well as between affected subjects and individuals at risk for OCD. PMID:18314272

  15. Alzheimer's disease neuroimaging initiative: a one-year follow up study using tensor-based morphometry correlating degenerative rates, biomarkers and cognition.

    PubMed

    Leow, Alex D; Yanovsky, Igor; Parikshak, Neelroop; Hua, Xue; Lee, Suh; Toga, Arthur W; Jack, Clifford R; Bernstein, Matt A; Britson, Paula J; Gunter, Jeffrey L; Ward, Chadwick P; Borowski, Bret; Shaw, Leslie M; Trojanowski, John Q; Fleisher, Adam S; Harvey, Danielle; Kornak, John; Schuff, Norbert; Alexander, Gene E; Weiner, Michael W; Thompson, Paul M

    2009-04-15

    Tensor-based morphometry can recover three-dimensional longitudinal brain changes over time by nonlinearly registering baseline to follow-up MRI scans of the same subject. Here, we compared the anatomical distribution of longitudinal brain structural changes, over 12 months, using a subset of the ADNI dataset consisting of 20 patients with Alzheimer's disease (AD), 40 healthy elderly controls, and 40 individuals with mild cognitive impairment (MCI). Each individual longitudinal change map (Jacobian map) was created using an unbiased registration technique, and spatially normalized to a geometrically-centered average image based on healthy controls. Voxelwise statistical analyses revealed regional differences in atrophy rates, and these differences were correlated with clinical measures and biomarkers. Consistent with prior studies, we detected widespread cerebral atrophy in AD, and a more restricted atrophic pattern in MCI. In MCI, temporal lobe atrophy rates were correlated with changes in mini-mental state exam (MMSE) scores, clinical dementia rating (CDR), and logical/verbal learning memory scores. In AD, temporal atrophy rates were correlated with several biomarker indices, including a higher CSF level of p-tau protein, and a greater CSF tau/beta amyloid 1-42 (ABeta42) ratio. Temporal lobe atrophy was significantly faster in MCI subjects who converted to AD than in non-converters. Serial MRI scans can therefore be analyzed with nonlinear image registration to relate ongoing neurodegeneration to a variety of pathological biomarkers, cognitive changes, and conversion from MCI to AD, tracking disease progression in 3-dimensional detail.

  16. Depressive symptoms and neuroanatomical structures in community-dwelling women: A combined voxel-based morphometry and diffusion tensor imaging study with tract-based spatial statistics.

    PubMed

    Hayakawa, Yayoi K; Sasaki, Hiroki; Takao, Hidemasa; Hayashi, Naoto; Kunimatsu, Akira; Ohtomo, Kuni; Aoki, Shigeki

    2014-01-01

    Depressive symptoms, even at a subclinical level, have been associated with structural brain abnormalities. However, previous studies have used regions of interest or small sample sizes, limiting the ability to generalize the results. In this study, we examined neuroanatomical structures of both gray matter and white matter associated with depressive symptoms across the whole brain in a large sample. A total of 810 community-dwelling adult participants underwent measurement of depressive symptoms with the Center for Epidemiologic Studies Depression Scale (CES-D). The participants were not demented and had no neurological or psychiatric history. To examine the gray and white matter volume, we used structural MRI scans and voxel-based morphometry (VBM); to examine the white matter integrity, we used diffusion tensor imaging with tract-based spatial statistics (TBSS). In female participants, VBM revealed a negative correlation between bilateral anterior cingulate gray matter volume and the CES-D score. TBSS showed a CES-D-related decrease in fractional anisotropy and increase in radial and mean diffusivity in several white matter regions, including the right anterior cingulum. In male participants, there was no significant correlation between gray or white matter volume or white matter integrity and the CES-D score. Our results indicate that the reduction in gray matter volume and differences in white matter integrity in specific brain regions, including the anterior cingulate, are associated with depressive symptoms in women.

  17. The Pivotal Role of the Parieto-Occipital Lobe in Card Game-Induced Reflex Epilepsy: A Voxel-Based Morphometry Study.

    PubMed

    Park, Kang Min; Kim, Sung Eun; Lee, Byung In

    2016-01-01

    The pathogenesis of card game-induced reflex epilepsy has not been determined so far. The aim of this study was to evaluate structural abnormalities using voxel-based morphometry (VBM) analysis, which may give some clue about the pathogenesis in card game-induced reflex epilepsy. The 3 subjects were diagnosed with card game-induced reflex epilepsy. Evaluation involved a structured interview to obtain clinical information and brain MRI. In VBM analysis, Statistical Parametric Mapping 8 running on the MATLAB platform was employed to analyze the structural differences between patients with card game-induced reflex epilepsy and age- and sex-matched control subjects. The results of VBM analysis revealed that patients with card game-induced reflex epilepsy had significantly increased gray matter volume in the right occipital and parietal lobe. However, there were no structures with decreased gray matter volume in patients with card game-induced reflex epilepsy compared with control subjects. In addition, we found that the patients with card game-induced reflex epilepsy had onset of seizures in adulthood rather than in adolescence, and all of the patients were men. The parieto-occipital lobes might be partially involved in the neuronal network responsible for card game-induced reflex epilepsy. © 2016 S. Karger AG, Basel.

  18. Brain morphometry and the neurobiology of levodopa-induced dyskinesias: current knowledge and future potential for translational pre-clinical neuroimaging studies.

    PubMed

    Finlay, Clare J; Duty, Susan; Vernon, Anthony C

    2014-01-01

    Dopamine replacement therapy in the form of levodopa results in a significant proportion of patients with Parkinson's disease developing debilitating dyskinesia. This significantly complicates further treatment and negatively impacts patient quality of life. A greater understanding of the neurobiological mechanisms underlying levodopa-induced dyskinesia (LID) is therefore crucial to develop new treatments to prevent or mitigate LID. Such investigations in humans are largely confined to assessment of neurochemical and cerebrovascular blood flow changes using positron emission tomography and functional magnetic resonance imaging. However, recent evidence suggests that LID is associated with specific morphological changes in the frontal cortex and midbrain, detectable by structural MRI and voxel-based morphometry. Current human neuroimaging methods however lack sufficient resolution to reveal the biological mechanism driving these morphological changes at the cellular level. In contrast, there is a wealth of literature from well-established rodent models of LID documenting detailed post-mortem cellular and molecular measurements. The combination therefore of advanced neuroimaging methods and rodent LID models offers an exciting opportunity to bridge these currently disparate areas of research. To highlight this opportunity, in this mini-review, we provide an overview of the current clinical evidence for morphological changes in the brain associated with LID and identify potential cellular mechanisms as suggested from human and animal studies. We then suggest a framework for combining small animal MRI imaging with rodent models of LID, which may provide important mechanistic insights into the neurobiology of LID.

  19. Role of morphometry in the cytological differentiation of benign and malignant thyroid lesions

    PubMed Central

    Khatri, Pallavi; Choudhury, Monisha; Jain, Manjula; Thomas, Shaji

    2017-01-01

    Context: Thyroid nodules represent a common problem, with an estimated prevalence of 4–7%. Although fine needle aspiration cytology (FNAC) has been accepted as a first line diagnostic test, the rate of false negative reports of malignancy is still high. Nuclear morphometry is the measurement of nuclear parameters by image analysis. Image analysis can merge the advantages of morphologic interpretation with those of quantitative data. Aims: To evaluate the nuclear morphometric parameters in fine needle aspirates of thyroid lesions and to study its role in differentiating benign from malignant thyroid lesions. Material and Methods: The study included 19 benign and 16 malignant thyroid lesions. Image analysis was performed on Giemsa-stained FNAC slides by Nikon NIS-Elements Advanced Research software (Version 4.00). Nuclear morphometric parameters analyzed included nuclear size, shape, texture, and density parameters. Statistical Analysis: Normally distributed continuous variables were compared using the unpaired t-test for two groups and analysis of variance was used for three or more groups. Tukey or Tamhane's T2 multiple comparison test was used to assess the differences between the individual groups. Categorical variables were analyzed using the chi square test. Results and Conclusion: Five out of the six nuclear size parameters as well as all the texture and density parameters studied were significant in distinguishing between benign and malignant thyroid lesions (P < 0.05). Cut-off values were derived to differentiate between benign and malignant cases. PMID:28182069

  20. Brain morphometry and intelligence quotient measurements in children with sickle cell disease.

    PubMed

    Chen, Rong; Pawlak, Mikolaj A; Flynn, Thomas B; Krejza, Jaroslaw; Herskovits, Edward H; Melhem, Elias R

    2009-12-01

    To verify the hypothesis that volume of regional gray matter accounts substantially for variability in intelligence quotient (IQ) score among children with sickle cell disease, who have no magnetic resonance visible infarcts. We studied 31 children with sickle cell disease, homozygous for hemoglobin S, with no history of stroke, no magnetic resonance signal-intensity abnormality, and transcranial Doppler velocities <170 cm/sec, with a T1-weighted magnetic resonance sequence and the Kaufman Brief Intelligence Test. On the basis of Kaufman Brief Intelligence Test, we classified these children into 2 groups: high and low IQ based on a median split. We then used an automated and novel Bayesian voxel-based morphometry technique, called Graphical-Model-Based Multivariate Analysis (GAMMA), to assess the probabilistic association between IQ score and regional gray matter volume. GAMMA found 1 region linking low IQ with smaller cortical gray matter volume. In comparison with the children in the high-IQ group, children in the low-IQ group had smaller regional gray matter volume in both frontal lobes, both temporal lobes, and both parietal lobes. In children with sickle cell disease, we found a linear association between IQ and regional gray matter volume. This finding suggests that some variance in intellectual ability in children with sickle cell disease is accounted for by regional variability of gray matter volume, which is independent of neuroradiological evidence of infarct.

  1. Neural correlates of post-conventional moral reasoning: a voxel-based morphometry study.

    PubMed

    Prehn, Kristin; Korczykowski, Marc; Rao, Hengyi; Fang, Zhuo; Detre, John A; Robertson, Diana C

    2015-01-01

    Going back to Kohlberg, moral development research affirms that people progress through different stages of moral reasoning as cognitive abilities mature. Individuals at a lower level of moral reasoning judge moral issues mainly based on self-interest (personal interests schema) or based on adherence to laws and rules (maintaining norms schema), whereas individuals at the post-conventional level judge moral issues based on deeper principles and shared ideals. However, the extent to which moral development is reflected in structural brain architecture remains unknown. To investigate this question, we used voxel-based morphometry and examined the brain structure in a sample of 67 Master of Business Administration (MBA) students. Subjects completed the Defining Issues Test (DIT-2) which measures moral development in terms of cognitive schema preference. Results demonstrate that subjects at the post-conventional level of moral reasoning were characterized by increased gray matter volume in the ventromedial prefrontal cortex and subgenual anterior cingulate cortex, compared with subjects at a lower level of moral reasoning. Our findings support an important role for both cognitive and emotional processes in moral reasoning and provide first evidence for individual differences in brain structure according to the stages of moral reasoning first proposed by Kohlberg decades ago.

  2. Neural Correlates of Post-Conventional Moral Reasoning: A Voxel-Based Morphometry Study

    PubMed Central

    Prehn, Kristin; Korczykowski, Marc; Rao, Hengyi; Fang, Zhuo; Detre, John A.; Robertson, Diana C.

    2015-01-01

    Going back to Kohlberg, moral development research affirms that people progress through different stages of moral reasoning as cognitive abilities mature. Individuals at a lower level of moral reasoning judge moral issues mainly based on self-interest (personal interests schema) or based on adherence to laws and rules (maintaining norms schema), whereas individuals at the post-conventional level judge moral issues based on deeper principles and shared ideals. However, the extent to which moral development is reflected in structural brain architecture remains unknown. To investigate this question, we used voxel-based morphometry and examined the brain structure in a sample of 67 Master of Business Administration (MBA) students. Subjects completed the Defining Issues Test (DIT-2) which measures moral development in terms of cognitive schema preference. Results demonstrate that subjects at the post-conventional level of moral reasoning were characterized by increased gray matter volume in the ventromedial prefrontal cortex and subgenual anterior cingulate cortex, compared with subjects at a lower level of moral reasoning. Our findings support an important role for both cognitive and emotional processes in moral reasoning and provide first evidence for individual differences in brain structure according to the stages of moral reasoning first proposed by Kohlberg decades ago. PMID:26039547

  3. Structural correlates of formal thought disorder in schizophrenia: An ultra-high field multivariate morphometry study

    PubMed Central

    Palaniyappan, Lena; Mahmood, Jenaid; Balain, Vijender; Mougin, Olivier; Gowland, Penny A.; Liddle, Peter F.

    2015-01-01

    Background Persistent formal thought disorder (FTD) is one of the most characteristic features of schizophrenia. Several neuroimaging studies report spatially distinct neuroanatomical changes in association with FTD. Given that most studies so far have employed a univariate localisation approach that obscures the study of covarying interregional relationships, the present study focussed on the multivariate systemic pattern of anatomical changes that contribute to FTD. Methods Speech samples from nineteen medicated clinically stable schizophrenia patients and 20 healthy controls were evaluated for subtle f